[PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor).

DoneSubmitted by zimoun.
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  • Ricardo Wurmus
  • zimoun
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zimoun wrote on 21 May 22:21 +0200
(address . guix-patches@gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202136.26524-1-zimon.toutoune@gmail.com
Hi,
Janitor [1] patch set. It moves Bioconductor packages from (gnu packagesbioinformatics) to (gnu packages bioconductor).
1: https://lists.gnu.org/archive/html/guix-commits/2020-09/msg00416.html

To transfer the Copyright, I use:
git --no-pager log --date=format:"%Y" --format="%ad %an %s" --grep=r-<name>
I did my best to preserve the copyright. But I do not guarantee it is error-free.Well, in doubt, I have been conservative.
Then, I do:
guix build r-<name> --no-grafts ./pre-inst-env guix build r-<name> --no-grafts --check
To avoid a break, I check with:
for ci in $(git log --format="%H" -51 --reverse); do ./pre-inst-env guix pull --commit=$ci \ -p /tmp/test-${ci} \ --url=$(pwd) --branch=janitor --disable-authentication done
and everyting seems fine. At least, "guix pull" should be checked at the endof the series.

Last, I have checked the imported modules in gnu/packages/bioinformatics.scm.All should be fine.
Now, I get:
Toggle snippet (6 lines)$ ag 'bioconductor' gnu/packages/bioinformatics.scm69: #:use-module (gnu packages bioconductor)11550: (synopsis "Extra base functions for Bioconductor")11553:provided by Bioconductor packages.")
which ends the move, I guess. Except the package r-rcurl ingnu/packages/statistics.scm, let as an exercise for the reader. ;-)

On a side note about the Copyright lines, I did:
git blame --date=format:"%Y)" gnu/packages/bioinformatics.scm \ | cut -d')' -f1 | cut -d'(' -f2 | sed 's/ //g' \ | sort | uniq -c
and it is possible that there is some "mistake", FWIW.
All the best,simon

zimoun (50): gnu: r-genomicalignments: Move to (gnu packages bioconductor). gnu: r-rtracklayer: Move to (gnu packages bioconductor). gnu: r-genomicfeatures: Move to (gnu packages bioconductor). gnu: r-topgo: Move to (gnu packages bioconductor). gnu: r-bsgenome: Move to (gnu packages bioconductor). gnu: r-msnid: Move to (gnu packages bioconductor). gnu: r-msnbase: Move to (gnu packages bioconductor). gnu: r-samr: Move to (gnu packages bioconductor). gnu: r-impute: Move to (gnu packages bioconductor). gnu: r-seqpattern: Move to (gnu packages bioconductor). gnu: r-go-db: Move to (gnu packages bioconductor). gnu: r-genomation: Move to (gnu packages bioconductor). gnu: r-genomationdata: Move to (gnu packages bioconductor). gnu: r-pcamethods: Move to (gnu packages bioconductor). gnu: r-mzid: Move to (gnu packages bioconductor). gnu: r-aroma-light: Move to (gnu packages bioconductor). gnu: r-deseq: Move to (gnu packages bioconductor). gnu: r-edaseq: Move to (gnu packages bioconductor). gnu: r-interactivedisplaybase: Move to (gnu packages bioconductor). gnu: r-annotationhub: Move to (gnu packages bioconductor). gnu: r-fastseg: Move to (gnu packages bioconductor). gnu: r-affy: Move to (gnu packages bioconductor). gnu: r-keggrest: Move to (gnu packages bioconductor). gnu: r-gage: Move to (gnu packages bioconductor). gnu: r-complexheatmap: Move to (gnu packages bioconductor). gnu: r-genomicfiles: Move to (gnu packages bioconductor). gnu: r-dirichletmultinomial: Move to (gnu packages bioconductor). gnu: r-organismdbi: Move to (gnu packages bioconductor). gnu: r-affyio: Move to (gnu packages bioconductor). gnu: r-vsn: Move to (gnu packages bioconductor). gnu: r-biovizbase: Move to (gnu packages bioconductor). gnu: r-ensembldb: Move to (gnu packages bioconductor). gnu: r-mzr: Move to (gnu packages bioconductor). gnu: r-protgenerics: Move to (gnu packages bioconductor). gnu: r-sva: Move to (gnu packages bioconductor). gnu: r-motifrg: Move to (gnu packages bioconductor). gnu: r-seqlogo: Move to (gnu packages bioconductor). gnu: r-zlibbioc: Move to (gnu packages bioconductor). gnu: r-rhtslib: Move to (gnu packages bioconductor). gnu: r-bamsignals: Move to (gnu packages bioconductor). gnu: r-rcas: Move to (gnu packages bioconductor). gnu: r-mutationalpatterns: Move to (gnu packages bioconductor). gnu: r-tximport: Move to (gnu packages bioconductor). gnu: r-rhdf5filters: Move to (gnu packages bioconductor). gnu: r-annotationfilter: Move to (gnu packages bioconductor). gnu: r-rhdf5: Move to (gnu packages bioconductor). gnu: r-chipseq: Move to (gnu packages bioconductor). gnu: r-copyhelper: Move to (gnu packages bioconductor). gnu: r-copywriter: Move to (gnu packages bioconductor). gnu: r-methylkit: Move to (gnu packages bioconductor).
gnu/packages/bioconductor.scm | 1826 +++++++++++++++++++++++++++++-- gnu/packages/bioinformatics.scm | 1645 ---------------------------- gnu/packages/cran.scm | 30 - 3 files changed, 1749 insertions(+), 1752 deletions(-)

base-commit: bd382fae71d899e243e81688bf5baed26171f2ea-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 02/50] gnu: r-rtracklayer: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-2-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-rtracklayer): Move from here...* gnu/packages/bioconductor.scm (r-rtracklayer): ...to here.--- gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 48 --------------------------------- 2 files changed, 48 insertions(+), 48 deletions(-)
Toggle diff (120 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 4f4ff82ad0..42a3d1fffc 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2385,6 +2385,54 @@ Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.") (license license:expat))) +(define-public r-rtracklayer+ (package+ (name "r-rtracklayer")+ (version "1.50.0")+ (source (origin+ (method url-fetch)+ (uri (bioconductor-uri "rtracklayer" version))+ (sha256+ (base32+ "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8"))))+ (build-system r-build-system)+ (arguments+ `(#:phases+ (modify-phases %standard-phases+ (add-after 'unpack 'use-system-zlib+ (lambda _+ (substitute* "DESCRIPTION"+ ((" zlibbioc,") ""))+ (substitute* "NAMESPACE"+ (("import\\(zlibbioc\\)") ""))+ #t)))))+ (native-inputs+ `(("pkg-config" ,pkg-config)))+ (inputs+ `(("zlib" ,zlib)))+ (propagated-inputs+ `(("r-biocgenerics" ,r-biocgenerics)+ ("r-biostrings" ,r-biostrings)+ ("r-genomeinfodb" ,r-genomeinfodb)+ ("r-genomicalignments" ,r-genomicalignments)+ ("r-genomicranges" ,r-genomicranges)+ ("r-iranges" ,r-iranges)+ ("r-rcurl" ,r-rcurl)+ ("r-rsamtools" ,r-rsamtools)+ ("r-s4vectors" ,r-s4vectors)+ ("r-xml" ,r-xml)+ ("r-xvector" ,r-xvector)+ ("r-zlibbioc" ,r-zlibbioc)))+ (home-page "https://bioconductor.org/packages/rtracklayer")+ (synopsis "R interface to genome browsers and their annotation tracks")+ (description+ "rtracklayer is an extensible framework for interacting with multiple+genome browsers (currently UCSC built-in) and manipulating annotation tracks+in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit+built-in). The user may export/import tracks to/from the supported browsers,+as well as query and modify the browser state, such as the current viewport.")+ (license license:artistic2.0)))+ (define-public r-shortread (package (name "r-shortread")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 0d0fe1df30..9fb46c0d5d 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -7849,54 +7849,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-rtracklayer- (package- (name "r-rtracklayer")- (version "1.50.0")- (source (origin- (method url-fetch)- (uri (bioconductor-uri "rtracklayer" version))- (sha256- (base32- "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8"))))- (build-system r-build-system)- (arguments- `(#:phases- (modify-phases %standard-phases- (add-after 'unpack 'use-system-zlib- (lambda _- (substitute* "DESCRIPTION"- ((" zlibbioc,") ""))- (substitute* "NAMESPACE"- (("import\\(zlibbioc\\)") ""))- #t)))))- (native-inputs- `(("pkg-config" ,pkg-config)))- (inputs- `(("zlib" ,zlib)))- (propagated-inputs- `(("r-biocgenerics" ,r-biocgenerics)- ("r-biostrings" ,r-biostrings)- ("r-genomeinfodb" ,r-genomeinfodb)- ("r-genomicalignments" ,r-genomicalignments)- ("r-genomicranges" ,r-genomicranges)- ("r-iranges" ,r-iranges)- ("r-rcurl" ,r-rcurl)- ("r-rsamtools" ,r-rsamtools)- ("r-s4vectors" ,r-s4vectors)- ("r-xml" ,r-xml)- ("r-xvector" ,r-xvector)- ("r-zlibbioc" ,r-zlibbioc)))- (home-page "https://bioconductor.org/packages/rtracklayer")- (synopsis "R interface to genome browsers and their annotation tracks")- (description- "rtracklayer is an extensible framework for interacting with multiple-genome browsers (currently UCSC built-in) and manipulating annotation tracks-in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit-built-in). The user may export/import tracks to/from the supported browsers,-as well as query and modify the browser state, such as the current viewport.")- (license license:artistic2.0)))- (define-public r-genomicfeatures (package (name "r-genomicfeatures")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 01/50] gnu: r-genomicalignments: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-1-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-genomicalignments): Move from here...* gnu/packages/bioconductor.scm (r-genomicalignments): ...to here.--- gnu/packages/bioconductor.scm | 35 ++++++++++++++++++++++++++++++++- gnu/packages/bioinformatics.scm | 33 ------------------------------- 2 files changed, 34 insertions(+), 34 deletions(-)
Toggle diff (97 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 45e31a5760..4f4ff82ad0 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU-;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>+;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org> ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>@@ -2075,6 +2075,39 @@ translation between different chromosome sequence naming conventions (e.g., names in their natural, rather than lexicographic, order.") (license license:artistic2.0))) +(define-public r-genomicalignments+ (package+ (name "r-genomicalignments")+ (version "1.26.0")+ (source (origin+ (method url-fetch)+ (uri (bioconductor-uri "GenomicAlignments" version))+ (sha256+ (base32+ "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr"))))+ (properties+ `((upstream-name . "GenomicAlignments")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-biocgenerics" ,r-biocgenerics)+ ("r-biocparallel" ,r-biocparallel)+ ("r-biostrings" ,r-biostrings)+ ("r-genomeinfodb" ,r-genomeinfodb)+ ("r-genomicranges" ,r-genomicranges)+ ("r-iranges" ,r-iranges)+ ("r-rsamtools" ,r-rsamtools)+ ("r-s4vectors" ,r-s4vectors)+ ("r-summarizedexperiment" ,r-summarizedexperiment)))+ (home-page "https://bioconductor.org/packages/GenomicAlignments")+ (synopsis "Representation and manipulation of short genomic alignments")+ (description+ "This package provides efficient containers for storing and manipulating+short genomic alignments (typically obtained by aligning short reads to a+reference genome). This includes read counting, computing the coverage,+junction detection, and working with the nucleotide content of the+alignments.")+ (license license:artistic2.0)))+ (define-public r-genomicranges (package (name "r-genomicranges")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 9c77d66a35..0d0fe1df30 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -7849,39 +7849,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-genomicalignments- (package- (name "r-genomicalignments")- (version "1.26.0")- (source (origin- (method url-fetch)- (uri (bioconductor-uri "GenomicAlignments" version))- (sha256- (base32- "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr"))))- (properties- `((upstream-name . "GenomicAlignments")))- (build-system r-build-system)- (propagated-inputs- `(("r-biocgenerics" ,r-biocgenerics)- ("r-biocparallel" ,r-biocparallel)- ("r-biostrings" ,r-biostrings)- ("r-genomeinfodb" ,r-genomeinfodb)- ("r-genomicranges" ,r-genomicranges)- ("r-iranges" ,r-iranges)- ("r-rsamtools" ,r-rsamtools)- ("r-s4vectors" ,r-s4vectors)- ("r-summarizedexperiment" ,r-summarizedexperiment)))- (home-page "https://bioconductor.org/packages/GenomicAlignments")- (synopsis "Representation and manipulation of short genomic alignments")- (description- "This package provides efficient containers for storing and manipulating-short genomic alignments (typically obtained by aligning short reads to a-reference genome). This includes read counting, computing the coverage,-junction detection, and working with the nucleotide content of the-alignments.")- (license license:artistic2.0)))- (define-public r-rtracklayer (package (name "r-rtracklayer")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 03/50] gnu: r-genomicfeatures: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-3-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Move from here...* gnu/packages/bioconductor.scm (r-genomicfeatures): ...to here.--- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 43 --------------------------------- 2 files changed, 43 insertions(+), 43 deletions(-)
Toggle diff (110 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 42a3d1fffc..2263c17cc4 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2108,6 +2108,49 @@ junction detection, and working with the nucleotide content of the alignments.") (license license:artistic2.0))) +(define-public r-genomicfeatures+ (package+ (name "r-genomicfeatures")+ (version "1.42.3")+ (source (origin+ (method url-fetch)+ (uri (bioconductor-uri "GenomicFeatures" version))+ (sha256+ (base32+ "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz"))))+ (properties+ `((upstream-name . "GenomicFeatures")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-annotationdbi" ,r-annotationdbi)+ ("r-biobase" ,r-biobase)+ ("r-biocgenerics" ,r-biocgenerics)+ ("r-biomart" ,r-biomart)+ ("r-biostrings" ,r-biostrings)+ ("r-dbi" ,r-dbi)+ ("r-genomeinfodb" ,r-genomeinfodb)+ ("r-genomicranges" ,r-genomicranges)+ ("r-iranges" ,r-iranges)+ ("r-rcurl" ,r-rcurl)+ ("r-rsqlite" ,r-rsqlite)+ ("r-rtracklayer" ,r-rtracklayer)+ ("r-s4vectors" ,r-s4vectors)+ ("r-xvector" ,r-xvector)))+ (native-inputs+ `(("r-knitr" ,r-knitr)))+ (home-page "https://bioconductor.org/packages/GenomicFeatures")+ (synopsis "Tools for working with transcript centric annotations")+ (description+ "This package provides a set of tools and methods for making and+manipulating transcript centric annotations. With these tools the user can+easily download the genomic locations of the transcripts, exons and cds of a+given organism, from either the UCSC Genome Browser or a BioMart+database (more sources will be supported in the future). This information is+then stored in a local database that keeps track of the relationship between+transcripts, exons, cds and genes. Flexible methods are provided for+extracting the desired features in a convenient format.")+ (license license:artistic2.0)))+ (define-public r-genomicranges (package (name "r-genomicranges")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 9fb46c0d5d..bf8cb2f3a5 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -7849,49 +7849,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-genomicfeatures- (package- (name "r-genomicfeatures")- (version "1.42.3")- (source (origin- (method url-fetch)- (uri (bioconductor-uri "GenomicFeatures" version))- (sha256- (base32- "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz"))))- (properties- `((upstream-name . "GenomicFeatures")))- (build-system r-build-system)- (propagated-inputs- `(("r-annotationdbi" ,r-annotationdbi)- ("r-biobase" ,r-biobase)- ("r-biocgenerics" ,r-biocgenerics)- ("r-biomart" ,r-biomart)- ("r-biostrings" ,r-biostrings)- ("r-dbi" ,r-dbi)- ("r-genomeinfodb" ,r-genomeinfodb)- ("r-genomicranges" ,r-genomicranges)- ("r-iranges" ,r-iranges)- ("r-rcurl" ,r-rcurl)- ("r-rsqlite" ,r-rsqlite)- ("r-rtracklayer" ,r-rtracklayer)- ("r-s4vectors" ,r-s4vectors)- ("r-xvector" ,r-xvector)))- (native-inputs- `(("r-knitr" ,r-knitr)))- (home-page "https://bioconductor.org/packages/GenomicFeatures")- (synopsis "Tools for working with transcript centric annotations")- (description- "This package provides a set of tools and methods for making and-manipulating transcript centric annotations. With these tools the user can-easily download the genomic locations of the transcripts, exons and cds of a-given organism, from either the UCSC Genome Browser or a BioMart-database (more sources will be supported in the future). This information is-then stored in a local database that keeps track of the relationship between-transcripts, exons, cds and genes. Flexible methods are provided for-extracting the desired features in a convenient format.")- (license license:artistic2.0)))- (define-public r-go-db (package (name "r-go-db")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 06/50] gnu: r-msnid: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-6-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-msnid): Move from here...* gnu/packages/bioconductor.scm (r-msnid): ...to here.--- gnu/packages/bioconductor.scm | 52 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 52 --------------------------------- 2 files changed, 52 insertions(+), 52 deletions(-)
Toggle diff (128 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 923413135b..b5787cb207 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2312,6 +2312,58 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-msnid+ (package+ (name "r-msnid")+ (version "1.24.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "MSnID" version))+ (sha256+ (base32+ "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d"))))+ (properties `((upstream-name . "MSnID")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-annotationdbi" ,r-annotationdbi)+ ("r-annotationhub" ,r-annotationhub)+ ("r-biobase" ,r-biobase)+ ("r-biocgenerics" ,r-biocgenerics)+ ("r-biocstyle" ,r-biocstyle)+ ("r-biostrings" ,r-biostrings)+ ("r-data-table" ,r-data-table)+ ("r-doparallel" ,r-doparallel)+ ("r-dplyr" ,r-dplyr)+ ("r-foreach" ,r-foreach)+ ("r-ggplot2" ,r-ggplot2)+ ("r-iterators" ,r-iterators)+ ("r-msnbase" ,r-msnbase)+ ("r-msmstests" ,r-msmstests)+ ("r-mzid" ,r-mzid)+ ("r-mzr" ,r-mzr)+ ("r-protgenerics" ,r-protgenerics)+ ("r-purrr" ,r-purrr)+ ("r-r-cache" ,r-r-cache)+ ("r-rcpp" ,r-rcpp)+ ("r-reshape2" ,r-reshape2)+ ("r-rlang" ,r-rlang)+ ("r-runit" ,r-runit)+ ("r-stringr" ,r-stringr)+ ("r-tibble" ,r-tibble)+ ("r-xtable" ,r-xtable)))+ (home-page "https://bioconductor.org/packages/MSnID")+ (synopsis "Utilities for LC-MSn proteomics identifications")+ (description+ "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data+from mzIdentML (leveraging the mzID package) or text files. After collating+the search results from multiple datasets it assesses their identification+quality and optimize filtering criteria to achieve the maximum number of+identifications while not exceeding a specified false discovery rate. It also+contains a number of utilities to explore the MS/MS results and assess missed+and irregular enzymatic cleavages, mass measurement accuracy, etc.")+ (license license:artistic2.0)))+ (define-public r-rbgl (package (name "r-rbgl")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 9c9288c6b0..5c2abe6e94 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -9275,58 +9275,6 @@ structure (pcaRes) to provide a common interface to the PCA results.") of mass spectrometry based proteomics data.") (license license:artistic2.0))) -(define-public r-msnid- (package- (name "r-msnid")- (version "1.24.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "MSnID" version))- (sha256- (base32- "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d"))))- (properties `((upstream-name . "MSnID")))- (build-system r-build-system)- (propagated-inputs- `(("r-annotationdbi" ,r-annotationdbi)- ("r-annotationhub" ,r-annotationhub)- ("r-biobase" ,r-biobase)- ("r-biocgenerics" ,r-biocgenerics)- ("r-biocstyle" ,r-biocstyle)- ("r-biostrings" ,r-biostrings)- ("r-data-table" ,r-data-table)- ("r-doparallel" ,r-doparallel)- ("r-dplyr" ,r-dplyr)- ("r-foreach" ,r-foreach)- ("r-ggplot2" ,r-ggplot2)- ("r-iterators" ,r-iterators)- ("r-msnbase" ,r-msnbase)- ("r-msmstests" ,r-msmstests)- ("r-mzid" ,r-mzid)- ("r-mzr" ,r-mzr)- ("r-protgenerics" ,r-protgenerics)- ("r-purrr" ,r-purrr)- ("r-r-cache" ,r-r-cache)- ("r-rcpp" ,r-rcpp)- ("r-reshape2" ,r-reshape2)- ("r-rlang" ,r-rlang)- ("r-runit" ,r-runit)- ("r-stringr" ,r-stringr)- ("r-tibble" ,r-tibble)- ("r-xtable" ,r-xtable)))- (home-page "https://bioconductor.org/packages/MSnID")- (synopsis "Utilities for LC-MSn proteomics identifications")- (description- "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data-from mzIdentML (leveraging the mzID package) or text files. After collating-the search results from multiple datasets it assesses their identification-quality and optimize filtering criteria to achieve the maximum number of-identifications while not exceeding a specified false discovery rate. It also-contains a number of utilities to explore the MS/MS results and assess missed-and irregular enzymatic cleavages, mass measurement accuracy, etc.")- (license license:artistic2.0)))- (define-public r-aroma-light (package (name "r-aroma-light")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 05/50] gnu: r-bsgenome: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-5-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-bsgenome): Move from here...* gnu/packages/bioconductor.scm (r-bsgenome): ...to here.--- gnu/packages/bioconductor.scm | 33 ++++++++++++++++++++++++++++++++- gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 32 insertions(+), 32 deletions(-)
Toggle diff (95 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 2afb5214ee..923413135b 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -4,7 +4,7 @@ ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>-;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>+;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com> ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>@@ -1875,6 +1875,37 @@ matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.") (license license:artistic2.0))) +(define-public r-bsgenome+ (package+ (name "r-bsgenome")+ (version "1.58.0")+ (source (origin+ (method url-fetch)+ (uri (bioconductor-uri "BSgenome" version))+ (sha256+ (base32+ "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq"))))+ (properties+ `((upstream-name . "BSgenome")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-biocgenerics" ,r-biocgenerics)+ ("r-biostrings" ,r-biostrings)+ ("r-genomeinfodb" ,r-genomeinfodb)+ ("r-genomicranges" ,r-genomicranges)+ ("r-iranges" ,r-iranges)+ ("r-matrixstats" ,r-matrixstats)+ ("r-rsamtools" ,r-rsamtools)+ ("r-rtracklayer" ,r-rtracklayer)+ ("r-s4vectors" ,r-s4vectors)+ ("r-xvector" ,r-xvector)))+ (home-page "https://bioconductor.org/packages/BSgenome")+ (synopsis "Infrastructure for Biostrings-based genome data packages")+ (description+ "This package provides infrastructure shared by all Biostrings-based+genome data packages and support for efficient SNP representation.")+ (license license:artistic2.0)))+ (define-public r-category (package (name "r-category")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 32d2b6a683..9c9288c6b0 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -7873,37 +7873,6 @@ including VCF header and contents in RDF and JSON.") information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) -(define-public r-bsgenome- (package- (name "r-bsgenome")- (version "1.58.0")- (source (origin- (method url-fetch)- (uri (bioconductor-uri "BSgenome" version))- (sha256- (base32- "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq"))))- (properties- `((upstream-name . "BSgenome")))- (build-system r-build-system)- (propagated-inputs- `(("r-biocgenerics" ,r-biocgenerics)- ("r-biostrings" ,r-biostrings)- ("r-genomeinfodb" ,r-genomeinfodb)- ("r-genomicranges" ,r-genomicranges)- ("r-iranges" ,r-iranges)- ("r-matrixstats" ,r-matrixstats)- ("r-rsamtools" ,r-rsamtools)- ("r-rtracklayer" ,r-rtracklayer)- ("r-s4vectors" ,r-s4vectors)- ("r-xvector" ,r-xvector)))- (home-page "https://bioconductor.org/packages/BSgenome")- (synopsis "Infrastructure for Biostrings-based genome data packages")- (description- "This package provides infrastructure shared by all Biostrings-based-genome data packages and support for efficient SNP representation.")- (license license:artistic2.0)))- (define-public r-impute (package (name "r-impute")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 07/50] gnu: r-msnbase: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-7-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-msnbase): Move from here...* gnu/packages/bioconductor.scm (r-msnbase): ...to here.--- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 45 --------------------------------- 2 files changed, 45 insertions(+), 45 deletions(-)
Toggle diff (114 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex b5787cb207..58c8336ce5 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2312,6 +2312,51 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-msnbase+ (package+ (name "r-msnbase")+ (version "2.16.1")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "MSnbase" version))+ (sha256+ (base32+ "0hxzs9zzljywqxr7q388hshpy1pdryhl0zkwffqbxpf5pcf92d3h"))))+ (properties `((upstream-name . "MSnbase")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-affy" ,r-affy)+ ("r-biobase" ,r-biobase)+ ("r-biocgenerics" ,r-biocgenerics)+ ("r-biocparallel" ,r-biocparallel)+ ("r-digest" ,r-digest)+ ("r-ggplot2" ,r-ggplot2)+ ("r-impute" ,r-impute)+ ("r-iranges" ,r-iranges)+ ("r-lattice" ,r-lattice)+ ("r-maldiquant" ,r-maldiquant)+ ("r-mass" ,r-mass)+ ("r-mzid" ,r-mzid)+ ("r-mzr" ,r-mzr)+ ("r-pcamethods" ,r-pcamethods)+ ("r-plyr" ,r-plyr)+ ("r-preprocesscore" ,r-preprocesscore)+ ("r-protgenerics" ,r-protgenerics)+ ("r-rcpp" ,r-rcpp)+ ("r-s4vectors" ,r-s4vectors)+ ("r-scales" ,r-scales)+ ("r-vsn" ,r-vsn)+ ("r-xml" ,r-xml)))+ (native-inputs+ `(("r-knitr" ,r-knitr)))+ (home-page "https://github.com/lgatto/MSnbase")+ (synopsis "Base functions and classes for MS-based proteomics")+ (description+ "This package provides basic plotting, data manipulation and processing+of mass spectrometry based proteomics data.")+ (license license:artistic2.0)))+ (define-public r-msnid (package (name "r-msnid")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 5c2abe6e94..28893c40e7 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -9230,51 +9230,6 @@ the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results.") (license license:gpl3+))) -(define-public r-msnbase- (package- (name "r-msnbase")- (version "2.16.1")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "MSnbase" version))- (sha256- (base32- "0hxzs9zzljywqxr7q388hshpy1pdryhl0zkwffqbxpf5pcf92d3h"))))- (properties `((upstream-name . "MSnbase")))- (build-system r-build-system)- (propagated-inputs- `(("r-affy" ,r-affy)- ("r-biobase" ,r-biobase)- ("r-biocgenerics" ,r-biocgenerics)- ("r-biocparallel" ,r-biocparallel)- ("r-digest" ,r-digest)- ("r-ggplot2" ,r-ggplot2)- ("r-impute" ,r-impute)- ("r-iranges" ,r-iranges)- ("r-lattice" ,r-lattice)- ("r-maldiquant" ,r-maldiquant)- ("r-mass" ,r-mass)- ("r-mzid" ,r-mzid)- ("r-mzr" ,r-mzr)- ("r-pcamethods" ,r-pcamethods)- ("r-plyr" ,r-plyr)- ("r-preprocesscore" ,r-preprocesscore)- ("r-protgenerics" ,r-protgenerics)- ("r-rcpp" ,r-rcpp)- ("r-s4vectors" ,r-s4vectors)- ("r-scales" ,r-scales)- ("r-vsn" ,r-vsn)- ("r-xml" ,r-xml)))- (native-inputs- `(("r-knitr" ,r-knitr)))- (home-page "https://github.com/lgatto/MSnbase")- (synopsis "Base functions and classes for MS-based proteomics")- (description- "This package provides basic plotting, data manipulation and processing-of mass spectrometry based proteomics data.")- (license license:artistic2.0)))- (define-public r-aroma-light (package (name "r-aroma-light")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 08/50] gnu: r-samr: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-8-zimon.toutoune@gmail.com
* gnu/packages/cran.scm (r-samr): Move from here...* gnu/packages/bioconductor.scm (r-samr): ...to here.--- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/cran.scm | 30 ------------------------------ 2 files changed, 31 insertions(+), 30 deletions(-)
Toggle diff (99 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 58c8336ce5..f9aa34d254 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -10,6 +10,7 @@ ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>+;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com> ;;; ;;; This file is part of GNU Guix. ;;;@@ -2604,6 +2605,36 @@ built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.") (license license:artistic2.0))) +;; This is a CRAN package, but it depends on a Bioconductor package.+(define-public r-samr+ (package+ (name "r-samr")+ (version "3.0")+ (source+ (origin+ (method url-fetch)+ (uri (cran-uri "samr" version))+ (sha256+ (base32+ "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))+ (properties `((upstream-name . "samr")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-gsa" ,r-gsa)+ ("r-impute" ,r-impute)+ ("r-matrixstats" ,r-matrixstats)+ ("r-openxlsx" ,r-openxlsx)+ ("r-shiny" ,r-shiny)+ ("r-shinyfiles" ,r-shinyfiles)))+ (native-inputs `(("gfortran" ,gfortran)))+ (home-page "https://statweb.stanford.edu/~tibs/SAM/")+ (synopsis "Significance analysis of Microarrays")+ (description+ "This is a package for significance analysis of Microarrays for+differential expression analysis, RNAseq data and related problems.")+ ;; Any version of the LGPL+ (license license:lgpl3+)))+ (define-public r-shortread (package (name "r-shortread")diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex 8709cd21fa..e5d1db7cb6 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -33,7 +33,6 @@ ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com> ;;; Copyright © 2020 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com>-;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com> ;;; ;;; This file is part of GNU Guix. ;;;@@ -28629,35 +28628,6 @@ indicator, a quantitative variable or a survival time.") ;; Any version of the LGPL (license license:lgpl3+))) -(define-public r-samr- (package- (name "r-samr")- (version "3.0")- (source- (origin- (method url-fetch)- (uri (cran-uri "samr" version))- (sha256- (base32- "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))- (properties `((upstream-name . "samr")))- (build-system r-build-system)- (propagated-inputs- `(("r-gsa" ,r-gsa)- ("r-impute" ,r-impute)- ("r-matrixstats" ,r-matrixstats)- ("r-openxlsx" ,r-openxlsx)- ("r-shiny" ,r-shiny)- ("r-shinyfiles" ,r-shinyfiles)))- (native-inputs `(("gfortran" ,gfortran)))- (home-page "https://statweb.stanford.edu/~tibs/SAM/")- (synopsis "Significance analysis of Microarrays")- (description- "This is a package for significance analysis of Microarrays for-differential expression analysis, RNAseq data and related problems.")- ;; Any version of the LGPL- (license license:lgpl3+)))- (define-public r-randomforestsrc (package (name "r-randomforestsrc")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 09/50] gnu: r-impute: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-9-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-impute): Move from here...* gnu/packages/bioconductor.scm (r-impute): ...to here.--- gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++ gnu/packages/bioinformatics.scm | 20 -------------------- 2 files changed, 20 insertions(+), 20 deletions(-)
Toggle diff (64 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex f9aa34d254..0b40d70397 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2294,6 +2294,26 @@ Enrichment Analysis} (GSEA).") the Human Protein Atlas project.") (license license:artistic2.0))) +(define-public r-impute+ (package+ (name "r-impute")+ (version "1.64.0")+ (source (origin+ (method url-fetch)+ (uri (bioconductor-uri "impute" version))+ (sha256+ (base32+ "1pnjasw9i19nmxwjzrd9jbln31yc5jilfvwk414ya5zbqfsazvxa"))))+ (native-inputs+ `(("gfortran" ,gfortran)))+ (build-system r-build-system)+ (home-page "https://bioconductor.org/packages/impute")+ (synopsis "Imputation for microarray data")+ (description+ "This package provides a function to impute missing gene expression+microarray data, using nearest neighbor averaging.")+ (license license:gpl2+)))+ (define-public r-limma (package (name "r-limma")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 28893c40e7..ef5c1a3323 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -7873,26 +7873,6 @@ including VCF header and contents in RDF and JSON.") information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) -(define-public r-impute- (package- (name "r-impute")- (version "1.64.0")- (source (origin- (method url-fetch)- (uri (bioconductor-uri "impute" version))- (sha256- (base32- "1pnjasw9i19nmxwjzrd9jbln31yc5jilfvwk414ya5zbqfsazvxa"))))- (native-inputs- `(("gfortran" ,gfortran)))- (build-system r-build-system)- (home-page "https://bioconductor.org/packages/impute")- (synopsis "Imputation for microarray data")- (description- "This package provides a function to impute missing gene expression-microarray data, using nearest neighbor averaging.")- (license license:gpl2+)))- (define-public r-seqpattern (package (name "r-seqpattern")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 10/50] gnu: r-seqpattern: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-10-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-seqpattern): Move from here...* gnu/packages/bioconductor.scm (r-seqpattern): ...to here.--- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-)
Toggle diff (78 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 0b40d70397..1b1b00cde0 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2655,6 +2655,33 @@ differential expression analysis, RNAseq data and related problems.") ;; Any version of the LGPL (license license:lgpl3+))) +(define-public r-seqpattern+ (package+ (name "r-seqpattern")+ (version "1.22.0")+ (source (origin+ (method url-fetch)+ (uri (bioconductor-uri "seqPattern" version))+ (sha256+ (base32+ "0j68n6fwycxjpl2va5fw7ajb123n758s2pq997d76dysxghmrlzq"))))+ (properties+ `((upstream-name . "seqPattern")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-biostrings" ,r-biostrings)+ ("r-genomicranges" ,r-genomicranges)+ ("r-iranges" ,r-iranges)+ ("r-kernsmooth" ,r-kernsmooth)+ ("r-plotrix" ,r-plotrix)))+ (home-page "https://bioconductor.org/packages/seqPattern")+ (synopsis "Visualising oligonucleotide patterns and motif occurrences")+ (description+ "This package provides tools to visualize oligonucleotide patterns and+sequence motif occurrences across a large set of sequences centred at a common+reference point and sorted by a user defined feature.")+ (license license:gpl3+)))+ (define-public r-shortread (package (name "r-shortread")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex ef5c1a3323..71e1481af2 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -7873,33 +7873,6 @@ including VCF header and contents in RDF and JSON.") information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) -(define-public r-seqpattern- (package- (name "r-seqpattern")- (version "1.22.0")- (source (origin- (method url-fetch)- (uri (bioconductor-uri "seqPattern" version))- (sha256- (base32- "0j68n6fwycxjpl2va5fw7ajb123n758s2pq997d76dysxghmrlzq"))))- (properties- `((upstream-name . "seqPattern")))- (build-system r-build-system)- (propagated-inputs- `(("r-biostrings" ,r-biostrings)- ("r-genomicranges" ,r-genomicranges)- ("r-iranges" ,r-iranges)- ("r-kernsmooth" ,r-kernsmooth)- ("r-plotrix" ,r-plotrix)))- (home-page "https://bioconductor.org/packages/seqPattern")- (synopsis "Visualising oligonucleotide patterns and motif occurrences")- (description- "This package provides tools to visualize oligonucleotide patterns and-sequence motif occurrences across a large set of sequences centred at a common-reference point and sorted by a user defined feature.")- (license license:gpl3+)))- (define-public r-genomation (package (name "r-genomation")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 11/50] gnu: r-go-db: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-11-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-go-db): Move from here...* gnu/packages/bioconductor.scm (r-go-db): ...to here.[source]: Replace 'string-append' by 'bioconductor-uri' with 'annotation.--- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 24 ------------------------ 2 files changed, 22 insertions(+), 24 deletions(-)
Toggle diff (70 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 1b1b00cde0..eb73909723 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -413,6 +413,28 @@ in Biostrings objects.") ID and species. It is used by functions in the GenomeInfoDb package.") (license license:artistic2.0))) +(define-public r-go-db+ (package+ (name "r-go-db")+ (version "3.7.0")+ (source (origin+ (method url-fetch)+ (uri (bioconductor-uri "GO.db" version 'annotation))+ (sha256+ (base32+ "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))+ (properties+ `((upstream-name . "GO.db")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-annotationdbi" ,r-annotationdbi)))+ (home-page "https://bioconductor.org/packages/GO.db")+ (synopsis "Annotation maps describing the entire Gene Ontology")+ (description+ "The purpose of this GO.db annotation package is to provide detailed+information about the latest version of the Gene Ontologies.")+ (license license:artistic2.0)))+ (define-public r-homo-sapiens (package (name "r-homo-sapiens")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 71e1481af2..71f07748b6 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -7849,30 +7849,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-go-db- (package- (name "r-go-db")- (version "3.7.0")- (source (origin- (method url-fetch)- (uri (string-append "https://www.bioconductor.org/packages/"- "release/data/annotation/src/contrib/GO.db_"- version ".tar.gz"))- (sha256- (base32- "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))- (properties- `((upstream-name . "GO.db")))- (build-system r-build-system)- (propagated-inputs- `(("r-annotationdbi" ,r-annotationdbi)))- (home-page "https://bioconductor.org/packages/GO.db")- (synopsis "Annotation maps describing the entire Gene Ontology")- (description- "The purpose of this GO.db annotation package is to provide detailed-information about the latest version of the Gene Ontologies.")- (license license:artistic2.0)))- (define-public r-genomation (package (name "r-genomation")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 12/50] gnu: r-genomation: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-12-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-genomation): Move from here...* gnu/packages/bioconductor.scm (r-genomation): ...to here.--- gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 48 --------------------------------- 2 files changed, 48 insertions(+), 48 deletions(-)
Toggle diff (120 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex eb73909723..2be7920770 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2099,6 +2099,54 @@ CAGE.") high-throughput sequencing experiments.") (license license:artistic2.0))) +(define-public r-genomation+ (package+ (name "r-genomation")+ (version "1.22.0")+ (source (origin+ (method url-fetch)+ (uri (bioconductor-uri "genomation" version))+ (sha256+ (base32+ "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g"))))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-biostrings" ,r-biostrings)+ ("r-bsgenome" ,r-bsgenome)+ ("r-data-table" ,r-data-table)+ ("r-genomeinfodb" ,r-genomeinfodb)+ ("r-genomicalignments" ,r-genomicalignments)+ ("r-genomicranges" ,r-genomicranges)+ ("r-ggplot2" ,r-ggplot2)+ ("r-gridbase" ,r-gridbase)+ ("r-impute" ,r-impute)+ ("r-iranges" ,r-iranges)+ ("r-matrixstats" ,r-matrixstats)+ ("r-plotrix" ,r-plotrix)+ ("r-plyr" ,r-plyr)+ ("r-rcpp" ,r-rcpp)+ ("r-readr" ,r-readr)+ ("r-reshape2" ,r-reshape2)+ ("r-rsamtools" ,r-rsamtools)+ ("r-rtracklayer" ,r-rtracklayer)+ ("r-runit" ,r-runit)+ ("r-s4vectors" ,r-s4vectors)+ ("r-seqpattern" ,r-seqpattern)))+ (native-inputs+ `(("r-knitr" ,r-knitr)))+ (home-page "https://bioinformatics.mdc-berlin.de/genomation/")+ (synopsis "Summary, annotation and visualization of genomic data")+ (description+ "This package provides a package for summary and annotation of genomic+intervals. Users can visualize and quantify genomic intervals over+pre-defined functional regions, such as promoters, exons, introns, etc. The+genomic intervals represent regions with a defined chromosome position, which+may be associated with a score, such as aligned reads from HT-seq experiments,+TF binding sites, methylation scores, etc. The package can use any tabular+genomic feature data as long as it has minimal information on the locations of+genomic intervals. In addition, it can use BAM or BigWig files as input.")+ (license license:artistic2.0)))+ (define-public r-genomeinfodb (package (name "r-genomeinfodb")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 71f07748b6..f8e7b2cab9 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -7849,54 +7849,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-genomation- (package- (name "r-genomation")- (version "1.22.0")- (source (origin- (method url-fetch)- (uri (bioconductor-uri "genomation" version))- (sha256- (base32- "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g"))))- (build-system r-build-system)- (propagated-inputs- `(("r-biostrings" ,r-biostrings)- ("r-bsgenome" ,r-bsgenome)- ("r-data-table" ,r-data-table)- ("r-genomeinfodb" ,r-genomeinfodb)- ("r-genomicalignments" ,r-genomicalignments)- ("r-genomicranges" ,r-genomicranges)- ("r-ggplot2" ,r-ggplot2)- ("r-gridbase" ,r-gridbase)- ("r-impute" ,r-impute)- ("r-iranges" ,r-iranges)- ("r-matrixstats" ,r-matrixstats)- ("r-plotrix" ,r-plotrix)- ("r-plyr" ,r-plyr)- ("r-rcpp" ,r-rcpp)- ("r-readr" ,r-readr)- ("r-reshape2" ,r-reshape2)- ("r-rsamtools" ,r-rsamtools)- ("r-rtracklayer" ,r-rtracklayer)- ("r-runit" ,r-runit)- ("r-s4vectors" ,r-s4vectors)- ("r-seqpattern" ,r-seqpattern)))- (native-inputs- `(("r-knitr" ,r-knitr)))- (home-page "https://bioinformatics.mdc-berlin.de/genomation/")- (synopsis "Summary, annotation and visualization of genomic data")- (description- "This package provides a package for summary and annotation of genomic-intervals. Users can visualize and quantify genomic intervals over-pre-defined functional regions, such as promoters, exons, introns, etc. The-genomic intervals represent regions with a defined chromosome position, which-may be associated with a score, such as aligned reads from HT-seq experiments,-TF binding sites, methylation scores, etc. The package can use any tabular-genomic feature data as long as it has minimal information on the locations of-genomic intervals. In addition, it can use BAM or BigWig files as input.")- (license license:artistic2.0)))- (define-public r-genomationdata (package (name "r-genomationdata")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 04/50] gnu: r-topgo: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-4-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-topgo): Move from here...* gnu/packages/bioconductor.scm (r-topgo): ...to here.--- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 33 --------------------------------- 2 files changed, 33 insertions(+), 33 deletions(-)
Toggle diff (90 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 2263c17cc4..2afb5214ee 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2607,6 +2607,39 @@ experimental designs is facilitated by a consistently implemented sample annotation infrastructure.") (license license:artistic2.0))) +(define-public r-topgo+ (package+ (name "r-topgo")+ (version "2.42.0")+ (source (origin+ (method url-fetch)+ (uri (bioconductor-uri "topGO" version))+ (sha256+ (base32+ "0vr3l9gvd3dhy446k3fkj6rm7z1abxi56rbnrs64297yzxaz1ngl"))))+ (properties+ `((upstream-name . "topGO")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-annotationdbi" ,r-annotationdbi)+ ("r-dbi" ,r-dbi)+ ("r-biobase" ,r-biobase)+ ("r-biocgenerics" ,r-biocgenerics)+ ("r-go-db" ,r-go-db)+ ("r-graph" ,r-graph)+ ("r-lattice" ,r-lattice)+ ("r-matrixstats" ,r-matrixstats)+ ("r-sparsem" ,r-sparsem)))+ (home-page "https://bioconductor.org/packages/topGO")+ (synopsis "Enrichment analysis for gene ontology")+ (description+ "The topGO package provides tools for testing @dfn{gene ontology} (GO)+terms while accounting for the topology of the GO graph. Different test+statistics and different methods for eliminating local similarities and+dependencies between GO terms can be implemented and applied.")+ ;; Any version of the LGPL applies.+ (license license:lgpl2.1+)))+ (define-public r-variantannotation (package (name "r-variantannotation")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex bf8cb2f3a5..32d2b6a683 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -7873,39 +7873,6 @@ including VCF header and contents in RDF and JSON.") information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) -(define-public r-topgo- (package- (name "r-topgo")- (version "2.42.0")- (source (origin- (method url-fetch)- (uri (bioconductor-uri "topGO" version))- (sha256- (base32- "0vr3l9gvd3dhy446k3fkj6rm7z1abxi56rbnrs64297yzxaz1ngl"))))- (properties- `((upstream-name . "topGO")))- (build-system r-build-system)- (propagated-inputs- `(("r-annotationdbi" ,r-annotationdbi)- ("r-dbi" ,r-dbi)- ("r-biobase" ,r-biobase)- ("r-biocgenerics" ,r-biocgenerics)- ("r-go-db" ,r-go-db)- ("r-graph" ,r-graph)- ("r-lattice" ,r-lattice)- ("r-matrixstats" ,r-matrixstats)- ("r-sparsem" ,r-sparsem)))- (home-page "https://bioconductor.org/packages/topGO")- (synopsis "Enrichment analysis for gene ontology")- (description- "The topGO package provides tools for testing @dfn{gene ontology} (GO)-terms while accounting for the topology of the GO graph. Different test-statistics and different methods for eliminating local similarities and-dependencies between GO terms can be implemented and applied.")- ;; Any version of the LGPL applies.- (license license:lgpl2.1+)))- (define-public r-bsgenome (package (name "r-bsgenome")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 13/50] gnu: r-genomationdata: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-13-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-genomationdata): Move from here...* gnu/packages/bioconductor.scm (r-genomationdata): ...to here.[source]: Replace 'string-append' by 'bioconductor-uri' with 'experiment.--- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 28 ---------------------------- 2 files changed, 26 insertions(+), 28 deletions(-)
Toggle diff (78 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 2be7920770..22b5a6068e 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -1021,6 +1021,32 @@ chromstaR package.") genomes and gene ID formats, largely based on the UCSC table browser.") (license license:lgpl2.0+))) +(define-public r-genomationdata+ (package+ (name "r-genomationdata")+ (version "1.22.0")+ (source (origin+ (method url-fetch)+ (uri (bioconductor-uri "genomationData" version 'experiment))+ (sha256+ (base32+ "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g"))))+ (properties+ `((upstream-name . "genomationData")))+ (build-system r-build-system)+ ;; As this package provides little more than large data files, it doesn't+ ;; make sense to build substitutes.+ (arguments `(#:substitutable? #f))+ (native-inputs+ `(("r-knitr" ,r-knitr)))+ (home-page "https://bioinformatics.mdc-berlin.de/genomation/")+ (synopsis "Experimental data for use with the genomation package")+ (description+ "This package contains experimental genetic data for use with the+genomation package. Included are Chip Seq, Methylation and Cage data,+downloaded from Encode.")+ (license license:gpl3+)))+ (define-public r-pasilla (package (name "r-pasilla")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex f8e7b2cab9..87254a9058 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -7849,34 +7849,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-genomationdata- (package- (name "r-genomationdata")- (version "1.22.0")- (source (origin- (method url-fetch)- ;; We cannot use bioconductor-uri here because this tarball is- ;; located under "data/annotation/" instead of "bioc/".- (uri (string-append "https://bioconductor.org/packages/"- "release/data/experiment/src/contrib/"- "genomationData_" version ".tar.gz"))- (sha256- (base32- "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g"))))- (build-system r-build-system)- ;; As this package provides little more than large data files, it doesn't- ;; make sense to build substitutes.- (arguments `(#:substitutable? #f))- (native-inputs- `(("r-knitr" ,r-knitr)))- (home-page "https://bioinformatics.mdc-berlin.de/genomation/")- (synopsis "Experimental data for use with the genomation package")- (description- "This package contains experimental genetic data for use with the-genomation package. Included are Chip Seq, Methylation and Cage data,-downloaded from Encode.")- (license license:gpl3+)))- (define-public r-seqlogo (package (name "r-seqlogo")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 14/50] gnu: r-pcamethods: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-14-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-pcamethods): Move from here...* gnu/packages/bioconductor.scm (r-pcamethods): ...to here.--- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-)
Toggle diff (84 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 22b5a6068e..1533e5b8f9 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2526,6 +2526,36 @@ contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.") (license license:artistic2.0))) +(define-public r-pcamethods+ (package+ (name "r-pcamethods")+ (version "1.82.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "pcaMethods" version))+ (sha256+ (base32+ "04xb4vjky6hq58l30i1iq9rv5gzjdxnidjxpnzg7pvg67vz8pgf0"))))+ (properties `((upstream-name . "pcaMethods")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-biobase" ,r-biobase)+ ("r-biocgenerics" ,r-biocgenerics)+ ("r-mass" ,r-mass)+ ("r-rcpp" ,r-rcpp)))+ (home-page "https://github.com/hredestig/pcamethods")+ (synopsis "Collection of PCA methods")+ (description+ "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,+Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method+for missing value estimation is included for comparison. BPCA, PPCA and+NipalsPCA may be used to perform PCA on incomplete data as well as for+accurate missing value estimation. A set of methods for printing and plotting+the results is also provided. All PCA methods make use of the same data+structure (pcaRes) to provide a common interface to the PCA results.")+ (license license:gpl3+)))+ (define-public r-rbgl (package (name "r-rbgl")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 87254a9058..a98f3d5d8a 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -9053,36 +9053,6 @@ mzIdentML files with the drawback of having less pretty output than a vendor specific parser.") (license license:gpl2+))) -(define-public r-pcamethods- (package- (name "r-pcamethods")- (version "1.82.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "pcaMethods" version))- (sha256- (base32- "04xb4vjky6hq58l30i1iq9rv5gzjdxnidjxpnzg7pvg67vz8pgf0"))))- (properties `((upstream-name . "pcaMethods")))- (build-system r-build-system)- (propagated-inputs- `(("r-biobase" ,r-biobase)- ("r-biocgenerics" ,r-biocgenerics)- ("r-mass" ,r-mass)- ("r-rcpp" ,r-rcpp)))- (home-page "https://github.com/hredestig/pcamethods")- (synopsis "Collection of PCA methods")- (description- "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,-Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method-for missing value estimation is included for comparison. BPCA, PPCA and-NipalsPCA may be used to perform PCA on incomplete data as well as for-accurate missing value estimation. A set of methods for printing and plotting-the results is also provided. All PCA methods make use of the same data-structure (pcaRes) to provide a common interface to the PCA results.")- (license license:gpl3+)))- (define-public r-aroma-light (package (name "r-aroma-light")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 15/50] gnu: r-mzid: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-15-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-mzid): Move from here...* gnu/packages/bioconductor.scm (r-mzid): ...to here.--- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-)
Toggle diff (86 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 1533e5b8f9..5e0b722e2f 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2526,6 +2526,37 @@ contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.") (license license:artistic2.0))) +(define-public r-mzid+ (package+ (name "r-mzid")+ (version "1.28.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "mzID" version))+ (sha256+ (base32+ "0s7d6cz1li7v3ni6n6hrdspl93yiyr283kmbbd3hhkfgzgx6kpq2"))))+ (properties `((upstream-name . "mzID")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-doparallel" ,r-doparallel)+ ("r-foreach" ,r-foreach)+ ("r-iterators" ,r-iterators)+ ("r-plyr" ,r-plyr)+ ("r-protgenerics" ,r-protgenerics)+ ("r-xml" ,r-xml)))+ (native-inputs+ `(("r-knitr" ,r-knitr)))+ (home-page "https://bioconductor.org/packages/mzID")+ (synopsis "Parser for mzIdentML files")+ (description+ "This package provides a parser for mzIdentML files implemented using the+XML package. The parser tries to be general and able to handle all types of+mzIdentML files with the drawback of having less pretty output than a vendor+specific parser.")+ (license license:gpl2+)))+ (define-public r-pcamethods (package (name "r-pcamethods")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex a98f3d5d8a..5b6426e17d 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -9022,37 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-mzid- (package- (name "r-mzid")- (version "1.28.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "mzID" version))- (sha256- (base32- "0s7d6cz1li7v3ni6n6hrdspl93yiyr283kmbbd3hhkfgzgx6kpq2"))))- (properties `((upstream-name . "mzID")))- (build-system r-build-system)- (propagated-inputs- `(("r-doparallel" ,r-doparallel)- ("r-foreach" ,r-foreach)- ("r-iterators" ,r-iterators)- ("r-plyr" ,r-plyr)- ("r-protgenerics" ,r-protgenerics)- ("r-xml" ,r-xml)))- (native-inputs- `(("r-knitr" ,r-knitr)))- (home-page "https://bioconductor.org/packages/mzID")- (synopsis "Parser for mzIdentML files")- (description- "This package provides a parser for mzIdentML files implemented using the-XML package. The parser tries to be general and able to handle all types of-mzIdentML files with the drawback of having less pretty output than a vendor-specific parser.")- (license license:gpl2+)))- (define-public r-aroma-light (package (name "r-aroma-light")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 16/50] gnu: r-aroma-light: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-16-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-aroma-light): Move from here...* gnu/packages/bioconductor.scm (r-aroma-light): ...to here.--- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-)
Toggle diff (78 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 5e0b722e2f..e58cd66fef 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -1782,6 +1782,33 @@ annotation data packages using SQLite data storage.") databases. Packages produced are intended to be used with AnnotationDbi.") (license license:artistic2.0))) +(define-public r-aroma-light+ (package+ (name "r-aroma-light")+ (version "3.20.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "aroma.light" version))+ (sha256+ (base32+ "0pi37rlfqh24p9wd7l1xb3f7c7938xdscgcc5agp8c9qhajq25a0"))))+ (properties `((upstream-name . "aroma.light")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-matrixstats" ,r-matrixstats)+ ("r-r-methodss3" ,r-r-methodss3)+ ("r-r-oo" ,r-r-oo)+ ("r-r-utils" ,r-r-utils)))+ (home-page "https://github.com/HenrikBengtsson/aroma.light")+ (synopsis "Methods for normalization and visualization of microarray data")+ (description+ "This package provides methods for microarray analysis that take basic+data types such as matrices and lists of vectors. These methods can be used+standalone, be utilized in other packages, or be wrapped up in higher-level+classes.")+ (license license:gpl2+)))+ (define-public r-biobase (package (name "r-biobase")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 5b6426e17d..c8444eea9f 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -9022,33 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-aroma-light- (package- (name "r-aroma-light")- (version "3.20.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "aroma.light" version))- (sha256- (base32- "0pi37rlfqh24p9wd7l1xb3f7c7938xdscgcc5agp8c9qhajq25a0"))))- (properties `((upstream-name . "aroma.light")))- (build-system r-build-system)- (propagated-inputs- `(("r-matrixstats" ,r-matrixstats)- ("r-r-methodss3" ,r-r-methodss3)- ("r-r-oo" ,r-r-oo)- ("r-r-utils" ,r-r-utils)))- (home-page "https://github.com/HenrikBengtsson/aroma.light")- (synopsis "Methods for normalization and visualization of microarray data")- (description- "This package provides methods for microarray analysis that take basic-data types such as matrices and lists of vectors. These methods can be used-standalone, be utilized in other packages, or be wrapped up in higher-level-classes.")- (license license:gpl2+)))- (define-public r-deseq (package (name "r-deseq")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 18/50] gnu: r-edaseq: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-18-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-edaseq): Move from here...* gnu/packages/bioconductor.scm (r-edaseq): ...to here.--- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 40 --------------------------------- 2 files changed, 40 insertions(+), 40 deletions(-)
Toggle diff (104 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 69ef513bc6..beb662984d 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2127,6 +2127,46 @@ testing. The package also provides functions for the visualization and exploration of the results.") (license license:gpl3+))) +(define-public r-edaseq+ (package+ (name "r-edaseq")+ (version "2.24.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "EDASeq" version))+ (sha256+ (base32+ "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip"))))+ (properties `((upstream-name . "EDASeq")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-annotationdbi" ,r-annotationdbi)+ ("r-aroma-light" ,r-aroma-light)+ ("r-biobase" ,r-biobase)+ ("r-biocgenerics" ,r-biocgenerics)+ ("r-biocmanager" ,r-biocmanager)+ ("r-biomart" ,r-biomart)+ ("r-biostrings" ,r-biostrings)+ ("r-genomicfeatures" ,r-genomicfeatures)+ ("r-genomicranges" ,r-genomicranges)+ ("r-iranges" ,r-iranges)+ ("r-rsamtools" ,r-rsamtools)+ ("r-shortread" ,r-shortread)))+ (native-inputs+ `(("r-knitr" ,r-knitr)))+ (home-page "https://github.com/drisso/EDASeq")+ (synopsis "Exploratory data analysis and normalization for RNA-Seq")+ (description+ "This package provides support for numerical and graphical summaries of+RNA-Seq genomic read data. Provided within-lane normalization procedures to+adjust for GC-content effect (or other gene-level effects) on read counts:+loess robust local regression, global-scaling, and full-quantile+normalization. Between-lane normalization procedures to adjust for+distributional differences between lanes (e.g., sequencing depth):+global-scaling and full-quantile normalization.")+ (license license:artistic2.0)))+ (define-public r-edger (package (name "r-edger")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 2edb501f9b..b0de0d9880 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -9022,46 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-edaseq- (package- (name "r-edaseq")- (version "2.24.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "EDASeq" version))- (sha256- (base32- "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip"))))- (properties `((upstream-name . "EDASeq")))- (build-system r-build-system)- (propagated-inputs- `(("r-annotationdbi" ,r-annotationdbi)- ("r-aroma-light" ,r-aroma-light)- ("r-biobase" ,r-biobase)- ("r-biocgenerics" ,r-biocgenerics)- ("r-biocmanager" ,r-biocmanager)- ("r-biomart" ,r-biomart)- ("r-biostrings" ,r-biostrings)- ("r-genomicfeatures" ,r-genomicfeatures)- ("r-genomicranges" ,r-genomicranges)- ("r-iranges" ,r-iranges)- ("r-rsamtools" ,r-rsamtools)- ("r-shortread" ,r-shortread)))- (native-inputs- `(("r-knitr" ,r-knitr)))- (home-page "https://github.com/drisso/EDASeq")- (synopsis "Exploratory data analysis and normalization for RNA-Seq")- (description- "This package provides support for numerical and graphical summaries of-RNA-Seq genomic read data. Provided within-lane normalization procedures to-adjust for GC-content effect (or other gene-level effects) on read counts:-loess robust local regression, global-scaling, and full-quantile-normalization. Between-lane normalization procedures to adjust for-distributional differences between lanes (e.g., sequencing depth):-global-scaling and full-quantile normalization.")- (license license:artistic2.0)))- (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 17/50] gnu: r-deseq: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-17-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-deseq): Move from here...* gnu/packages/bioconductor.scm (r-deseq): ...to here.--- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-)
Toggle diff (86 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex e58cd66fef..69ef513bc6 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2013,6 +2013,37 @@ genome data packages and support for efficient SNP representation.") analysis.") (license license:artistic2.0))) +(define-public r-deseq+ (package+ (name "r-deseq")+ (version "1.39.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "DESeq" version))+ (sha256+ (base32+ "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1"))))+ (properties `((upstream-name . "DESeq")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-biobase" ,r-biobase)+ ("r-biocgenerics" ,r-biocgenerics)+ ("r-genefilter" ,r-genefilter)+ ("r-geneplotter" ,r-geneplotter)+ ("r-lattice" ,r-lattice)+ ("r-locfit" ,r-locfit)+ ("r-mass" ,r-mass)+ ("r-rcolorbrewer" ,r-rcolorbrewer)))+ (home-page "https://www-huber.embl.de/users/anders/DESeq/")+ (synopsis "Differential gene expression analysis")+ (description+ "This package provides tools for estimating variance-mean dependence in+count data from high-throughput genetic sequencing assays and for testing for+differential expression based on a model using the negative binomial+distribution.")+ (license license:gpl3+)))+ (define-public r-deseq2 (package (name "r-deseq2")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex c8444eea9f..2edb501f9b 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -9022,37 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-deseq- (package- (name "r-deseq")- (version "1.39.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "DESeq" version))- (sha256- (base32- "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1"))))- (properties `((upstream-name . "DESeq")))- (build-system r-build-system)- (propagated-inputs- `(("r-biobase" ,r-biobase)- ("r-biocgenerics" ,r-biocgenerics)- ("r-genefilter" ,r-genefilter)- ("r-geneplotter" ,r-geneplotter)- ("r-lattice" ,r-lattice)- ("r-locfit" ,r-locfit)- ("r-mass" ,r-mass)- ("r-rcolorbrewer" ,r-rcolorbrewer)))- (home-page "https://www-huber.embl.de/users/anders/DESeq/")- (synopsis "Differential gene expression analysis")- (description- "This package provides tools for estimating variance-mean dependence in-count data from high-throughput genetic sequencing assays and for testing for-differential expression based on a model using the negative binomial-distribution.")- (license license:gpl3+)))- (define-public r-edaseq (package (name "r-edaseq")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 19/50] gnu: r-interactivedisplaybase: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-19-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Move from here...* gnu/packages/bioconductor.scm (r-interactivedisplaybase): ...to here.--- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-)
Toggle diff (78 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex beb662984d..9619ce5464 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2508,6 +2508,33 @@ the Human Protein Atlas project.") microarray data, using nearest neighbor averaging.") (license license:gpl2+))) +(define-public r-interactivedisplaybase+ (package+ (name "r-interactivedisplaybase")+ (version "1.28.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "interactiveDisplayBase" version))+ (sha256+ (base32+ "08id2hkx4ssxj34dildx00a4j3z0nv171b7b0wl6xjks7wk6lv01"))))+ (properties+ `((upstream-name . "interactiveDisplayBase")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-biocgenerics" ,r-biocgenerics)+ ("r-dt" ,r-dt)+ ("r-shiny" ,r-shiny)))+ (native-inputs+ `(("r-knitr" ,r-knitr)))+ (home-page "https://bioconductor.org/packages/interactiveDisplayBase")+ (synopsis "Base package for web displays of Bioconductor objects")+ (description+ "This package contains the basic methods needed to generate interactive+Shiny-based display methods for Bioconductor objects.")+ (license license:artistic2.0)))+ (define-public r-limma (package (name "r-limma")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex b0de0d9880..b367dcae98 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -9022,33 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-interactivedisplaybase- (package- (name "r-interactivedisplaybase")- (version "1.28.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "interactiveDisplayBase" version))- (sha256- (base32- "08id2hkx4ssxj34dildx00a4j3z0nv171b7b0wl6xjks7wk6lv01"))))- (properties- `((upstream-name . "interactiveDisplayBase")))- (build-system r-build-system)- (propagated-inputs- `(("r-biocgenerics" ,r-biocgenerics)- ("r-dt" ,r-dt)- ("r-shiny" ,r-shiny)))- (native-inputs- `(("r-knitr" ,r-knitr)))- (home-page "https://bioconductor.org/packages/interactiveDisplayBase")- (synopsis "Base package for web displays of Bioconductor objects")- (description- "This package contains the basic methods needed to generate interactive-Shiny-based display methods for Bioconductor objects.")- (license license:artistic2.0)))- (define-public r-annotationhub (package (name "r-annotationhub")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 20/50] gnu: r-annotationhub: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-20-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-annotationhub): Move from here...* gnu/packages/bioconductor.scm (r-annotationhub): ...to here.--- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 41 --------------------------------- 2 files changed, 41 insertions(+), 41 deletions(-)
Toggle diff (106 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 9619ce5464..4657b0fa8b 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -1782,6 +1782,47 @@ annotation data packages using SQLite data storage.") databases. Packages produced are intended to be used with AnnotationDbi.") (license license:artistic2.0))) +(define-public r-annotationhub+ (package+ (name "r-annotationhub")+ (version "2.22.1")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "AnnotationHub" version))+ (sha256+ (base32+ "08d7m0n4jkpajsj0bvi5xd4vi1zqczl6lnrh8kqi2fbjkrvwdqp5"))))+ (properties `((upstream-name . "AnnotationHub")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-annotationdbi" ,r-annotationdbi)+ ("r-biocfilecache" ,r-biocfilecache)+ ("r-biocgenerics" ,r-biocgenerics)+ ("r-biocmanager" ,r-biocmanager)+ ("r-biocversion" ,r-biocversion)+ ("r-curl" ,r-curl)+ ("r-dplyr" ,r-dplyr)+ ("r-httr" ,r-httr)+ ("r-interactivedisplaybase" ,r-interactivedisplaybase)+ ("r-rappdirs" ,r-rappdirs)+ ("r-rsqlite" ,r-rsqlite)+ ("r-s4vectors" ,r-s4vectors)+ ("r-yaml" ,r-yaml)))+ (native-inputs+ `(("r-knitr" ,r-knitr)))+ (home-page "https://bioconductor.org/packages/AnnotationHub")+ (synopsis "Client to access AnnotationHub resources")+ (description+ "This package provides a client for the Bioconductor AnnotationHub web+resource. The AnnotationHub web resource provides a central location where+genomic files (e.g. VCF, bed, wig) and other resources from standard+locations (e.g. UCSC, Ensembl) can be discovered. The resource includes+metadata about each resource, e.g., a textual description, tags, and date of+modification. The client creates and manages a local cache of files retrieved+by the user, helping with quick and reproducible access.")+ (license license:artistic2.0)))+ (define-public r-aroma-light (package (name "r-aroma-light")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex b367dcae98..1dc2d6f977 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -9022,47 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-annotationhub- (package- (name "r-annotationhub")- (version "2.22.1")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "AnnotationHub" version))- (sha256- (base32- "08d7m0n4jkpajsj0bvi5xd4vi1zqczl6lnrh8kqi2fbjkrvwdqp5"))))- (properties `((upstream-name . "AnnotationHub")))- (build-system r-build-system)- (propagated-inputs- `(("r-annotationdbi" ,r-annotationdbi)- ("r-biocfilecache" ,r-biocfilecache)- ("r-biocgenerics" ,r-biocgenerics)- ("r-biocmanager" ,r-biocmanager)- ("r-biocversion" ,r-biocversion)- ("r-curl" ,r-curl)- ("r-dplyr" ,r-dplyr)- ("r-httr" ,r-httr)- ("r-interactivedisplaybase" ,r-interactivedisplaybase)- ("r-rappdirs" ,r-rappdirs)- ("r-rsqlite" ,r-rsqlite)- ("r-s4vectors" ,r-s4vectors)- ("r-yaml" ,r-yaml)))- (native-inputs- `(("r-knitr" ,r-knitr)))- (home-page "https://bioconductor.org/packages/AnnotationHub")- (synopsis "Client to access AnnotationHub resources")- (description- "This package provides a client for the Bioconductor AnnotationHub web-resource. The AnnotationHub web resource provides a central location where-genomic files (e.g. VCF, bed, wig) and other resources from standard-locations (e.g. UCSC, Ensembl) can be discovered. The resource includes-metadata about each resource, e.g., a textual description, tags, and date of-modification. The client creates and manages a local cache of files retrieved-by the user, helping with quick and reproducible access.")- (license license:artistic2.0)))- (define-public r-fastseg (package (name "r-fastseg")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 21/50] gnu: r-fastseg: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-21-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-fastseg): Move from here...* gnu/packages/bioconductor.scm (r-fastseg): ...to here.--- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-)
Toggle diff (84 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 4657b0fa8b..313ed7e36f 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2236,6 +2236,36 @@ other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.") (license license:gpl2+))) +(define-public r-fastseg+ (package+ (name "r-fastseg")+ (version "1.36.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "fastseg" version))+ (sha256+ (base32+ "1ln6w93ag4wanp0nrm0pqngbfc88w95zq2kcj583hbxy885dkg4f"))))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-biobase" ,r-biobase)+ ("r-biocgenerics" ,r-biocgenerics)+ ("r-genomicranges" ,r-genomicranges)+ ("r-iranges" ,r-iranges)+ ("r-s4vectors" ,r-s4vectors)))+ (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")+ (synopsis "Fast segmentation algorithm for genetic sequencing data")+ (description+ "Fastseg implements a very fast and efficient segmentation algorithm.+It can segment data from DNA microarrays and data from next generation+sequencing for example to detect copy number segments. Further it can segment+data from RNA microarrays like tiling arrays to identify transcripts. Most+generally, it can segment data given as a matrix or as a vector. Various data+formats can be used as input to fastseg like expression set objects for+microarrays or GRanges for sequencing data.")+ (license license:lgpl2.0+)))+ (define-public r-genefilter (package (name "r-genefilter")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 1dc2d6f977..33680c283d 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -9022,36 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-fastseg- (package- (name "r-fastseg")- (version "1.36.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "fastseg" version))- (sha256- (base32- "1ln6w93ag4wanp0nrm0pqngbfc88w95zq2kcj583hbxy885dkg4f"))))- (build-system r-build-system)- (propagated-inputs- `(("r-biobase" ,r-biobase)- ("r-biocgenerics" ,r-biocgenerics)- ("r-genomicranges" ,r-genomicranges)- ("r-iranges" ,r-iranges)- ("r-s4vectors" ,r-s4vectors)))- (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")- (synopsis "Fast segmentation algorithm for genetic sequencing data")- (description- "Fastseg implements a very fast and efficient segmentation algorithm.-It can segment data from DNA microarrays and data from next generation-sequencing for example to detect copy number segments. Further it can segment-data from RNA microarrays like tiling arrays to identify transcripts. Most-generally, it can segment data given as a matrix or as a vector. Various data-formats can be used as input to fastseg like expression set objects for-microarrays or GRanges for sequencing data.")- (license license:lgpl2.0+)))- (define-public r-keggrest (package (name "r-keggrest")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 22/50] gnu: r-affy: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-22-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-affy): Move from here...* gnu/packages/bioconductor.scm (r-affy): ...to here.--- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 28 ---------------------------- 2 files changed, 28 insertions(+), 28 deletions(-)
Toggle diff (80 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 313ed7e36f..6d60b5884c 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -1550,6 +1550,34 @@ optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.") (license license:gpl2+))) +(define-public r-affy+ (package+ (name "r-affy")+ (version "1.68.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "affy" version))+ (sha256+ (base32+ "0ywz548cbzk2k1njnxhlk5ydzvz2dk78ka8kx53gwrmdc4sc2b06"))))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-affyio" ,r-affyio)+ ("r-biobase" ,r-biobase)+ ("r-biocgenerics" ,r-biocgenerics)+ ("r-biocmanager" ,r-biocmanager)+ ("r-preprocesscore" ,r-preprocesscore)+ ("r-zlibbioc" ,r-zlibbioc)))+ (inputs+ `(("zlib" ,zlib)))+ (home-page "https://bioconductor.org/packages/affy")+ (synopsis "Methods for affymetrix oligonucleotide arrays")+ (description+ "This package contains functions for exploratory oligonucleotide array+analysis.")+ (license license:lgpl2.0+)))+ (define-public r-affycomp (package (name "r-affycomp")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 33680c283d..b789ecd977 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -8958,34 +8958,6 @@ upon file format information. The primary focus is on accessing the CEL and CDF file formats.") (license license:lgpl2.0+))) -(define-public r-affy- (package- (name "r-affy")- (version "1.68.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "affy" version))- (sha256- (base32- "0ywz548cbzk2k1njnxhlk5ydzvz2dk78ka8kx53gwrmdc4sc2b06"))))- (build-system r-build-system)- (propagated-inputs- `(("r-affyio" ,r-affyio)- ("r-biobase" ,r-biobase)- ("r-biocgenerics" ,r-biocgenerics)- ("r-biocmanager" ,r-biocmanager)- ("r-preprocesscore" ,r-preprocesscore)- ("r-zlibbioc" ,r-zlibbioc)))- (inputs- `(("zlib" ,zlib)))- (home-page "https://bioconductor.org/packages/affy")- (synopsis "Methods for affymetrix oligonucleotide arrays")- (description- "This package contains functions for exploratory oligonucleotide array-analysis.")- (license license:lgpl2.0+)))- (define-public r-vsn (package (name "r-vsn")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 23/50] gnu: r-keggrest: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-23-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-keggrest): Move from here...* gnu/packages/bioconductor.scm (r-keggrest): ...to here.--- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 26 insertions(+), 26 deletions(-)
Toggle diff (76 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 6d60b5884c..5ee670e858 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2634,6 +2634,32 @@ microarray data, using nearest neighbor averaging.") Shiny-based display methods for Bioconductor objects.") (license license:artistic2.0))) +(define-public r-keggrest+ (package+ (name "r-keggrest")+ (version "1.30.1")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "KEGGREST" version))+ (sha256+ (base32+ "0k9z85xf9la2y98xqmdmjb8mci9fh2fdybkl77x1yl26hyalip0s"))))+ (properties `((upstream-name . "KEGGREST")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-biostrings" ,r-biostrings)+ ("r-httr" ,r-httr)+ ("r-png" ,r-png)))+ (native-inputs+ `(("r-knitr" ,r-knitr)))+ (home-page "https://bioconductor.org/packages/KEGGREST")+ (synopsis "Client-side REST access to KEGG")+ (description+ "This package provides a package that provides a client interface to the+@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")+ (license license:artistic2.0)))+ (define-public r-limma (package (name "r-limma")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex b789ecd977..5dacf8a342 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -8994,32 +8994,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-keggrest- (package- (name "r-keggrest")- (version "1.30.1")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "KEGGREST" version))- (sha256- (base32- "0k9z85xf9la2y98xqmdmjb8mci9fh2fdybkl77x1yl26hyalip0s"))))- (properties `((upstream-name . "KEGGREST")))- (build-system r-build-system)- (propagated-inputs- `(("r-biostrings" ,r-biostrings)- ("r-httr" ,r-httr)- ("r-png" ,r-png)))- (native-inputs- `(("r-knitr" ,r-knitr)))- (home-page "https://bioconductor.org/packages/KEGGREST")- (synopsis "Client-side REST access to KEGG")- (description- "This package provides a package that provides a client interface to the-@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")- (license license:artistic2.0)))- (define-public r-gage (package (name "r-gage")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 24/50] gnu: r-gage: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-24-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-gage): Move from here...* gnu/packages/bioconductor.scm (r-gage): ...to here.--- gnu/packages/bioconductor.scm | 33 ++++++++++++++++++++++++++++++++- gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 32 insertions(+), 32 deletions(-)
Toggle diff (95 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 5ee670e858..f6d3ef897a 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -4,7 +4,7 @@ ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>-;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>+;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com> ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>@@ -2294,6 +2294,37 @@ formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data.") (license license:lgpl2.0+))) +(define-public r-gage+ (package+ (name "r-gage")+ (version "2.40.2")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "gage" version))+ (sha256+ (base32+ "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178"))))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-annotationdbi" ,r-annotationdbi)+ ("r-go-db" ,r-go-db)+ ("r-graph" ,r-graph)+ ("r-keggrest" ,r-keggrest)))+ (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"+ "articles/10.1186/1471-2105-10-161"))+ (synopsis "Generally applicable gene-set enrichment for pathway analysis")+ (description+ "GAGE is a published method for gene set (enrichment or GSEA) or pathway+analysis. GAGE is generally applicable independent of microarray or RNA-Seq+data attributes including sample sizes, experimental designs, assay platforms,+and other types of heterogeneity. The gage package provides functions for+basic GAGE analysis, result processing and presentation. In addition, it+provides demo microarray data and commonly used gene set data based on KEGG+pathways and GO terms. These functions and data are also useful for gene set+analysis using other methods.")+ (license license:gpl2+)))+ (define-public r-genefilter (package (name "r-genefilter")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 5dacf8a342..daf1fb6958 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -8994,37 +8994,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-gage- (package- (name "r-gage")- (version "2.40.2")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "gage" version))- (sha256- (base32- "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178"))))- (build-system r-build-system)- (propagated-inputs- `(("r-annotationdbi" ,r-annotationdbi)- ("r-go-db" ,r-go-db)- ("r-graph" ,r-graph)- ("r-keggrest" ,r-keggrest)))- (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"- "articles/10.1186/1471-2105-10-161"))- (synopsis "Generally applicable gene-set enrichment for pathway analysis")- (description- "GAGE is a published method for gene set (enrichment or GSEA) or pathway-analysis. GAGE is generally applicable independent of microarray or RNA-Seq-data attributes including sample sizes, experimental designs, assay platforms,-and other types of heterogeneity. The gage package provides functions for-basic GAGE analysis, result processing and presentation. In addition, it-provides demo microarray data and commonly used gene set data based on KEGG-pathways and GO terms. These functions and data are also useful for gene set-analysis using other methods.")- (license license:gpl2+)))- (define-public r-genomicfiles (package (name "r-genomicfiles")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 25/50] gnu: r-complexheatmap: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-25-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-complexheatmap): Move from here...* gnu/packages/bioconductor.scm (r-complexheatmap): ...to here.--- gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 39 --------------------------------- 2 files changed, 39 insertions(+), 39 deletions(-)
Toggle diff (102 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex f6d3ef897a..92eb5a0906 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2082,6 +2082,45 @@ genome data packages and support for efficient SNP representation.") analysis.") (license license:artistic2.0))) +(define-public r-complexheatmap+ (package+ (name "r-complexheatmap")+ (version "2.6.2")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "ComplexHeatmap" version))+ (sha256+ (base32+ "1nx1xxpq8zrvi990v9fmvx3msl85pdz5dp1gp6m78q6i4s2alg5x"))))+ (properties+ `((upstream-name . "ComplexHeatmap")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-cairo" ,r-cairo)+ ("r-circlize" ,r-circlize)+ ("r-clue" ,r-clue)+ ("r-colorspace" ,r-colorspace)+ ("r-digest" ,r-digest)+ ("r-getoptlong" ,r-getoptlong)+ ("r-globaloptions" ,r-globaloptions)+ ("r-iranges" ,r-iranges)+ ("r-matrixstats" ,r-matrixstats)+ ("r-png" ,r-png)+ ("r-rcolorbrewer" ,r-rcolorbrewer)+ ("r-s4vectors" ,r-s4vectors)))+ (native-inputs+ `(("r-knitr" ,r-knitr)))+ (home-page+ "https://github.com/jokergoo/ComplexHeatmap")+ (synopsis "Making Complex Heatmaps")+ (description+ "Complex heatmaps are efficient to visualize associations between+different sources of data sets and reveal potential structures. This package+provides a highly flexible way to arrange multiple heatmaps and supports+self-defined annotation graphics.")+ (license license:gpl2+)))+ (define-public r-deseq (package (name "r-deseq")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex daf1fb6958..acaf41acc4 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -9028,45 +9028,6 @@ distributed by file or by range. User defined mapper and reducer functions provide added flexibility for data combination and manipulation.") (license license:artistic2.0))) -(define-public r-complexheatmap- (package- (name "r-complexheatmap")- (version "2.6.2")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "ComplexHeatmap" version))- (sha256- (base32- "1nx1xxpq8zrvi990v9fmvx3msl85pdz5dp1gp6m78q6i4s2alg5x"))))- (properties- `((upstream-name . "ComplexHeatmap")))- (build-system r-build-system)- (propagated-inputs- `(("r-cairo" ,r-cairo)- ("r-circlize" ,r-circlize)- ("r-clue" ,r-clue)- ("r-colorspace" ,r-colorspace)- ("r-digest" ,r-digest)- ("r-getoptlong" ,r-getoptlong)- ("r-globaloptions" ,r-globaloptions)- ("r-iranges" ,r-iranges)- ("r-matrixstats" ,r-matrixstats)- ("r-png" ,r-png)- ("r-rcolorbrewer" ,r-rcolorbrewer)- ("r-s4vectors" ,r-s4vectors)))- (native-inputs- `(("r-knitr" ,r-knitr)))- (home-page- "https://github.com/jokergoo/ComplexHeatmap")- (synopsis "Making Complex Heatmaps")- (description- "Complex heatmaps are efficient to visualize associations between-different sources of data sets and reveal potential structures. This package-provides a highly flexible way to arrange multiple heatmaps and supports-self-defined annotation graphics.")- (license license:gpl2+)))- (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 26/50] gnu: r-genomicfiles: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-26-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-genomicfiles): Move from here...* gnu/packages/bioconductor.scm (r-genomicfiles): ...to here.--- gnu/packages/bioconductor.scm | 34 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 34 --------------------------------- 2 files changed, 34 insertions(+), 34 deletions(-)
Toggle diff (92 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 92eb5a0906..e73e78f616 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2546,6 +2546,40 @@ transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.") (license license:artistic2.0))) +(define-public r-genomicfiles+ (package+ (name "r-genomicfiles")+ (version "1.26.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "GenomicFiles" version))+ (sha256+ (base32+ "0awnf0m1pz7cw9wvh9cfxz9k7xm6wnvjm7xbxf139lrhd4nlyqjz"))))+ (properties `((upstream-name . "GenomicFiles")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-biocgenerics" ,r-biocgenerics)+ ("r-biocparallel" ,r-biocparallel)+ ("r-genomeinfodb" ,r-genomeinfodb)+ ("r-genomicalignments" ,r-genomicalignments)+ ("r-genomicranges" ,r-genomicranges)+ ("r-iranges" ,r-iranges)+ ("r-matrixgenerics" ,r-matrixgenerics)+ ("r-rsamtools" ,r-rsamtools)+ ("r-rtracklayer" ,r-rtracklayer)+ ("r-s4vectors" ,r-s4vectors)+ ("r-summarizedexperiment" ,r-summarizedexperiment)+ ("r-variantannotation" ,r-variantannotation)))+ (home-page "https://bioconductor.org/packages/GenomicFiles")+ (synopsis "Distributed computing by file or by range")+ (description+ "This package provides infrastructure for parallel computations+distributed by file or by range. User defined mapper and reducer functions+provide added flexibility for data combination and manipulation.")+ (license license:artistic2.0)))+ (define-public r-genomicranges (package (name "r-genomicranges")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex acaf41acc4..4836eee82c 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -8994,40 +8994,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-genomicfiles- (package- (name "r-genomicfiles")- (version "1.26.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "GenomicFiles" version))- (sha256- (base32- "0awnf0m1pz7cw9wvh9cfxz9k7xm6wnvjm7xbxf139lrhd4nlyqjz"))))- (properties `((upstream-name . "GenomicFiles")))- (build-system r-build-system)- (propagated-inputs- `(("r-biocgenerics" ,r-biocgenerics)- ("r-biocparallel" ,r-biocparallel)- ("r-genomeinfodb" ,r-genomeinfodb)- ("r-genomicalignments" ,r-genomicalignments)- ("r-genomicranges" ,r-genomicranges)- ("r-iranges" ,r-iranges)- ("r-matrixgenerics" ,r-matrixgenerics)- ("r-rsamtools" ,r-rsamtools)- ("r-rtracklayer" ,r-rtracklayer)- ("r-s4vectors" ,r-s4vectors)- ("r-summarizedexperiment" ,r-summarizedexperiment)- ("r-variantannotation" ,r-variantannotation)))- (home-page "https://bioconductor.org/packages/GenomicFiles")- (synopsis "Distributed computing by file or by range")- (description- "This package provides infrastructure for parallel computations-distributed by file or by range. User defined mapper and reducer functions-provide added flexibility for data combination and manipulation.")- (license license:artistic2.0)))- (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial")-- 2.30.1
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zimoun wrote on 21 May 22:25 +0200
[PATCH 27/50] gnu: r-dirichletmultinomial: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-27-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Move from here...* gnu/packages/bioconductor.scm (r-dirichletmultinomial): ...to here.--- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 29 ----------------------------- 2 files changed, 29 insertions(+), 29 deletions(-)
Toggle diff (82 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex e73e78f616..7717c821b9 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2235,6 +2235,35 @@ testing. The package also provides functions for the visualization and exploration of the results.") (license license:gpl3+))) +(define-public r-dirichletmultinomial+ (package+ (name "r-dirichletmultinomial")+ (version "1.32.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "DirichletMultinomial" version))+ (sha256+ (base32+ "098zql6ryd1b0gkq4cjybblyh0x8xidxxfygqq5a5x9asl8y4vsk"))))+ (properties+ `((upstream-name . "DirichletMultinomial")))+ (build-system r-build-system)+ (inputs+ `(("gsl" ,gsl)))+ (propagated-inputs+ `(("r-biocgenerics" ,r-biocgenerics)+ ("r-iranges" ,r-iranges)+ ("r-s4vectors" ,r-s4vectors)))+ (home-page "https://bioconductor.org/packages/DirichletMultinomial")+ (synopsis "Dirichlet-Multinomial mixture models for microbiome data")+ (description+ "Dirichlet-multinomial mixture models can be used to describe variability+in microbial metagenomic data. This package is an interface to code+originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):+1-15.")+ (license license:lgpl3)))+ (define-public r-edaseq (package (name "r-edaseq")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 4836eee82c..0c7b3d602f 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -8994,35 +8994,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-dirichletmultinomial- (package- (name "r-dirichletmultinomial")- (version "1.32.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "DirichletMultinomial" version))- (sha256- (base32- "098zql6ryd1b0gkq4cjybblyh0x8xidxxfygqq5a5x9asl8y4vsk"))))- (properties- `((upstream-name . "DirichletMultinomial")))- (build-system r-build-system)- (inputs- `(("gsl" ,gsl)))- (propagated-inputs- `(("r-biocgenerics" ,r-biocgenerics)- ("r-iranges" ,r-iranges)- ("r-s4vectors" ,r-s4vectors)))- (home-page "https://bioconductor.org/packages/DirichletMultinomial")- (synopsis "Dirichlet-Multinomial mixture models for microbiome data")- (description- "Dirichlet-multinomial mixture models can be used to describe variability-in microbial metagenomic data. This package is an interface to code-originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):-1-15.")- (license license:lgpl3)))- (define-public r-ensembldb (package (name "r-ensembldb")-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 28/50] gnu: r-organismdbi: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-28-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-organismdbi): Move from here...* gnu/packages/bioconductor.scm (r-organismdbi): ...to here.--- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 32 -------------------------------- 2 files changed, 32 insertions(+), 32 deletions(-)
Toggle diff (88 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 7717c821b9..c63d39dc9c 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2940,6 +2940,38 @@ mzIdentML files with the drawback of having less pretty output than a vendor specific parser.") (license license:gpl2+))) +(define-public r-organismdbi+ (package+ (name "r-organismdbi")+ (version "1.32.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "OrganismDbi" version))+ (sha256+ (base32+ "1mklnzs0d0ygcdibwfnk5xqr8ln6wpa00qcaw9c68m342kql0jqw"))))+ (properties `((upstream-name . "OrganismDbi")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-annotationdbi" ,r-annotationdbi)+ ("r-biobase" ,r-biobase)+ ("r-biocgenerics" ,r-biocgenerics)+ ("r-biocmanager" ,r-biocmanager)+ ("r-dbi" ,r-dbi)+ ("r-genomicfeatures" ,r-genomicfeatures)+ ("r-genomicranges" ,r-genomicranges)+ ("r-graph" ,r-graph)+ ("r-iranges" ,r-iranges)+ ("r-rbgl" ,r-rbgl)+ ("r-s4vectors" ,r-s4vectors)))+ (home-page "https://bioconductor.org/packages/OrganismDbi")+ (synopsis "Software to enable the smooth interfacing of database packages")+ (description "The package enables a simple unified interface to several+annotation packages each of which has its own schema by taking advantage of+the fact that each of these packages implements a select methods.")+ (license license:artistic2.0)))+ (define-public r-pcamethods (package (name "r-pcamethods")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 0c7b3d602f..1c90700c95 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -9039,38 +9039,6 @@ chromosome region or transcript models of lincRNA genes.") ;; No version specified (license license:lgpl3+))) -(define-public r-organismdbi- (package- (name "r-organismdbi")- (version "1.32.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "OrganismDbi" version))- (sha256- (base32- "1mklnzs0d0ygcdibwfnk5xqr8ln6wpa00qcaw9c68m342kql0jqw"))))- (properties `((upstream-name . "OrganismDbi")))- (build-system r-build-system)- (propagated-inputs- `(("r-annotationdbi" ,r-annotationdbi)- ("r-biobase" ,r-biobase)- ("r-biocgenerics" ,r-biocgenerics)- ("r-biocmanager" ,r-biocmanager)- ("r-dbi" ,r-dbi)- ("r-genomicfeatures" ,r-genomicfeatures)- ("r-genomicranges" ,r-genomicranges)- ("r-graph" ,r-graph)- ("r-iranges" ,r-iranges)- ("r-rbgl" ,r-rbgl)- ("r-s4vectors" ,r-s4vectors)))- (home-page "https://bioconductor.org/packages/OrganismDbi")- (synopsis "Software to enable the smooth interfacing of database packages")- (description "The package enables a simple unified interface to several-annotation packages each of which has its own schema by taking advantage of-the fact that each of these packages implements a select methods.")- (license license:artistic2.0)))- (define-public r-biovizbase (package (name "r-biovizbase")-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 30/50] gnu: r-vsn: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-30-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-vsn): Move from here...* gnu/packages/bioconductor.scm (r-vsn): ...to here.--- gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 36 --------------------------------- 2 files changed, 36 insertions(+), 36 deletions(-)
Toggle diff (96 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex d0ebcf8481..05c4896276 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -3480,6 +3480,42 @@ dependencies between GO terms can be implemented and applied.") coding changes and predict coding outcomes.") (license license:artistic2.0))) +(define-public r-vsn+ (package+ (name "r-vsn")+ (version "3.58.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "vsn" version))+ (sha256+ (base32+ "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb"))))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-affy" ,r-affy)+ ("r-biobase" ,r-biobase)+ ("r-ggplot2" ,r-ggplot2)+ ("r-lattice" ,r-lattice)+ ("r-limma" ,r-limma)))+ (native-inputs+ `(("r-knitr" ,r-knitr))) ; for vignettes+ (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")+ (synopsis "Variance stabilization and calibration for microarray data")+ (description+ "The package implements a method for normalising microarray intensities,+and works for single- and multiple-color arrays. It can also be used for data+from other technologies, as long as they have similar format. The method uses+a robust variant of the maximum-likelihood estimator for an+additive-multiplicative error model and affine calibration. The model+incorporates data calibration step (a.k.a. normalization), a model for the+dependence of the variance on the mean intensity and a variance stabilizing+data transformation. Differences between transformed intensities are+analogous to \"normalized log-ratios\". However, in contrast to the latter,+their variance is independent of the mean, and they are usually more sensitive+and specific in detecting differential transcription.")+ (license license:artistic2.0)))+ (define-public r-xvector (package (name "r-xvector")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 7256df3f83..600c2ca81e 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -8934,42 +8934,6 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.") (license license:artistic2.0))) -(define-public r-vsn- (package- (name "r-vsn")- (version "3.58.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "vsn" version))- (sha256- (base32- "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb"))))- (build-system r-build-system)- (propagated-inputs- `(("r-affy" ,r-affy)- ("r-biobase" ,r-biobase)- ("r-ggplot2" ,r-ggplot2)- ("r-lattice" ,r-lattice)- ("r-limma" ,r-limma)))- (native-inputs- `(("r-knitr" ,r-knitr))) ; for vignettes- (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")- (synopsis "Variance stabilization and calibration for microarray data")- (description- "The package implements a method for normalising microarray intensities,-and works for single- and multiple-color arrays. It can also be used for data-from other technologies, as long as they have similar format. The method uses-a robust variant of the maximum-likelihood estimator for an-additive-multiplicative error model and affine calibration. The model-incorporates data calibration step (a.k.a. normalization), a model for the-dependence of the variance on the mean intensity and a variance stabilizing-data transformation. Differences between transformed intensities are-analogous to \"normalized log-ratios\". However, in contrast to the latter,-their variance is independent of the mean, and they are usually more sensitive-and specific in detecting differential transcription.")- (license license:artistic2.0)))- (define-public r-ensembldb (package (name "r-ensembldb")-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 31/50] gnu: r-biovizbase: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-31-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-biovizbase): Move from here...* gnu/packages/bioconductor.scm (r-biovizbase): ...to here.--- gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 42 --------------------------------- 2 files changed, 42 insertions(+), 42 deletions(-)
Toggle diff (108 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 05c4896276..7439ad96da 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2044,6 +2044,48 @@ matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.") (license license:artistic2.0))) +(define-public r-biovizbase+ (package+ (name "r-biovizbase")+ (version "1.38.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "biovizBase" version))+ (sha256+ (base32+ "10jflvadfcgxq2jnfxkpn417xd8ibh3zllz9rsqnq5w3wgfr4fhq"))))+ (properties `((upstream-name . "biovizBase")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-annotationdbi" ,r-annotationdbi)+ ("r-annotationfilter" ,r-annotationfilter)+ ("r-biocgenerics" ,r-biocgenerics)+ ("r-biostrings" ,r-biostrings)+ ("r-dichromat" ,r-dichromat)+ ("r-ensembldb" ,r-ensembldb)+ ("r-genomeinfodb" ,r-genomeinfodb)+ ("r-genomicalignments" ,r-genomicalignments)+ ("r-genomicfeatures" ,r-genomicfeatures)+ ("r-genomicranges" ,r-genomicranges)+ ("r-hmisc" ,r-hmisc)+ ("r-iranges" ,r-iranges)+ ("r-rcolorbrewer" ,r-rcolorbrewer)+ ("r-rlang" ,r-rlang)+ ("r-rsamtools" ,r-rsamtools)+ ("r-s4vectors" ,r-s4vectors)+ ("r-scales" ,r-scales)+ ("r-summarizedexperiment" ,r-summarizedexperiment)+ ("r-variantannotation" ,r-variantannotation)))+ (home-page "https://bioconductor.org/packages/biovizBase")+ (synopsis "Basic graphic utilities for visualization of genomic data")+ (description+ "The biovizBase package is designed to provide a set of utilities, color+schemes and conventions for genomic data. It serves as the base for various+high-level packages for biological data visualization. This saves development+effort and encourages consistency.")+ (license license:artistic2.0)))+ (define-public r-bsgenome (package (name "r-bsgenome")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 600c2ca81e..e6692ece0c 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -8979,48 +8979,6 @@ chromosome region or transcript models of lincRNA genes.") ;; No version specified (license license:lgpl3+))) -(define-public r-biovizbase- (package- (name "r-biovizbase")- (version "1.38.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "biovizBase" version))- (sha256- (base32- "10jflvadfcgxq2jnfxkpn417xd8ibh3zllz9rsqnq5w3wgfr4fhq"))))- (properties `((upstream-name . "biovizBase")))- (build-system r-build-system)- (propagated-inputs- `(("r-annotationdbi" ,r-annotationdbi)- ("r-annotationfilter" ,r-annotationfilter)- ("r-biocgenerics" ,r-biocgenerics)- ("r-biostrings" ,r-biostrings)- ("r-dichromat" ,r-dichromat)- ("r-ensembldb" ,r-ensembldb)- ("r-genomeinfodb" ,r-genomeinfodb)- ("r-genomicalignments" ,r-genomicalignments)- ("r-genomicfeatures" ,r-genomicfeatures)- ("r-genomicranges" ,r-genomicranges)- ("r-hmisc" ,r-hmisc)- ("r-iranges" ,r-iranges)- ("r-rcolorbrewer" ,r-rcolorbrewer)- ("r-rlang" ,r-rlang)- ("r-rsamtools" ,r-rsamtools)- ("r-s4vectors" ,r-s4vectors)- ("r-scales" ,r-scales)- ("r-summarizedexperiment" ,r-summarizedexperiment)- ("r-variantannotation" ,r-variantannotation)))- (home-page "https://bioconductor.org/packages/biovizBase")- (synopsis "Basic graphic utilities for visualization of genomic data")- (description- "The biovizBase package is designed to provide a set of utilities, color-schemes and conventions for genomic data. It serves as the base for various-high-level packages for biological data visualization. This saves development-effort and encourages consistency.")- (license license:artistic2.0)))- (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2"))-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 32/50] gnu: r-ensembldb: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-32-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-ensembldb): Move from here...* gnu/packages/bioconductor.scm (r-ensembldb): ...to here.--- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 45 --------------------------------- 2 files changed, 45 insertions(+), 45 deletions(-)
Toggle diff (114 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 7439ad96da..7e86af7d21 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2398,6 +2398,51 @@ other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.") (license license:gpl2+))) +(define-public r-ensembldb+ (package+ (name "r-ensembldb")+ (version "2.14.1")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "ensembldb" version))+ (sha256+ (base32+ "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40"))))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-annotationdbi" ,r-annotationdbi)+ ("r-annotationfilter" ,r-annotationfilter)+ ("r-biobase" ,r-biobase)+ ("r-biocgenerics" ,r-biocgenerics)+ ("r-biostrings" ,r-biostrings)+ ("r-curl" ,r-curl)+ ("r-dbi" ,r-dbi)+ ("r-genomeinfodb" ,r-genomeinfodb)+ ("r-genomicfeatures" ,r-genomicfeatures)+ ("r-genomicranges" ,r-genomicranges)+ ("r-iranges" ,r-iranges)+ ("r-protgenerics" ,r-protgenerics)+ ("r-rsamtools" ,r-rsamtools)+ ("r-rsqlite" ,r-rsqlite)+ ("r-rtracklayer" ,r-rtracklayer)+ ("r-s4vectors" ,r-s4vectors)))+ (native-inputs+ `(("r-knitr" ,r-knitr)))+ (home-page "https://github.com/jotsetung/ensembldb")+ (synopsis "Utilities to create and use Ensembl-based annotation databases")+ (description+ "The package provides functions to create and use transcript-centric+annotation databases/packages. The annotation for the databases are directly+fetched from Ensembl using their Perl API. The functionality and data is+similar to that of the TxDb packages from the @code{GenomicFeatures} package,+but, in addition to retrieve all gene/transcript models and annotations from+the database, the @code{ensembldb} package also provides a filter framework+allowing to retrieve annotations for specific entries like genes encoded on a+chromosome region or transcript models of lincRNA genes.")+ ;; No version specified+ (license license:lgpl3+)))+ (define-public r-fastseg (package (name "r-fastseg")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex e6692ece0c..baef88cd2e 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -8934,51 +8934,6 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.") (license license:artistic2.0))) -(define-public r-ensembldb- (package- (name "r-ensembldb")- (version "2.14.1")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "ensembldb" version))- (sha256- (base32- "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40"))))- (build-system r-build-system)- (propagated-inputs- `(("r-annotationdbi" ,r-annotationdbi)- ("r-annotationfilter" ,r-annotationfilter)- ("r-biobase" ,r-biobase)- ("r-biocgenerics" ,r-biocgenerics)- ("r-biostrings" ,r-biostrings)- ("r-curl" ,r-curl)- ("r-dbi" ,r-dbi)- ("r-genomeinfodb" ,r-genomeinfodb)- ("r-genomicfeatures" ,r-genomicfeatures)- ("r-genomicranges" ,r-genomicranges)- ("r-iranges" ,r-iranges)- ("r-protgenerics" ,r-protgenerics)- ("r-rsamtools" ,r-rsamtools)- ("r-rsqlite" ,r-rsqlite)- ("r-rtracklayer" ,r-rtracklayer)- ("r-s4vectors" ,r-s4vectors)))- (native-inputs- `(("r-knitr" ,r-knitr)))- (home-page "https://github.com/jotsetung/ensembldb")- (synopsis "Utilities to create and use Ensembl-based annotation databases")- (description- "The package provides functions to create and use transcript-centric-annotation databases/packages. The annotation for the databases are directly-fetched from Ensembl using their Perl API. The functionality and data is-similar to that of the TxDb packages from the @code{GenomicFeatures} package,-but, in addition to retrieve all gene/transcript models and annotations from-the database, the @code{ensembldb} package also provides a filter framework-allowing to retrieve annotations for specific entries like genes encoded on a-chromosome region or transcript models of lincRNA genes.")- ;; No version specified- (license license:lgpl3+)))- (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2"))-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 33/50] gnu: r-mzr: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-33-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-mzr): Move from here...* gnu/packages/bioconductor.scm (r-mzr): ...to here.--- gnu/packages/bioconductor.scm | 62 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 61 -------------------------------- 2 files changed, 62 insertions(+), 61 deletions(-)
Toggle diff (154 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 7e86af7d21..5ceffd7b4d 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -36,6 +36,7 @@ #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics)+ #:use-module (gnu packages boost) #:use-module (gnu packages cran) #:use-module (gnu packages compression) #:use-module (gnu packages gcc)@@ -3051,6 +3052,67 @@ mzIdentML files with the drawback of having less pretty output than a vendor specific parser.") (license license:gpl2+))) +(define-public r-mzr+ (package+ (name "r-mzr")+ (version "2.24.1")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "mzR" version))+ (sha256+ (base32+ "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg"))+ (modules '((guix build utils)))+ (snippet+ '(begin+ (delete-file-recursively "src/boost")+ #t))))+ (properties `((upstream-name . "mzR")))+ (build-system r-build-system)+ (arguments+ `(#:phases+ (modify-phases %standard-phases+ (add-after 'unpack 'use-system-boost+ (lambda _+ (substitute* "src/Makevars"+ (("\\./boost/libs.*") "")+ ;; This is to avoid having a plain directory on the list of+ ;; libraries to link.+ (("\\(RHDF5_LIBS\\)" match)+ (string-append match "/libhdf5.a"))+ (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")+ (("\\ARCH_OBJS=" line)+ (string-append line+ "\nBOOST_LIBS=-lboost_system -lboost_regex \+-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))+ #t)))))+ (inputs+ `(;; Our default boost package won't work here, unfortunately, even with+ ;; mzR version 2.24.1.+ ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources+ ("zlib" ,zlib)))+ (propagated-inputs+ `(("r-biobase" ,r-biobase)+ ("r-biocgenerics" ,r-biocgenerics)+ ("r-ncdf4" ,r-ncdf4)+ ("r-protgenerics" ,r-protgenerics)+ ("r-rcpp" ,r-rcpp)+ ("r-rhdf5lib" ,r-rhdf5lib)+ ("r-zlibbioc" ,r-zlibbioc)))+ (native-inputs+ `(("r-knitr" ,r-knitr)))+ (home-page "https://github.com/sneumann/mzR/")+ (synopsis "Parser for mass spectrometry data files")+ (description+ "The mzR package provides a unified API to the common file formats and+parsers available for mass spectrometry data. It comes with a wrapper for the+ISB random access parser for mass spectrometry mzXML, mzData and mzML files.+The package contains the original code written by the ISB, and a subset of the+proteowizard library for mzML and mzIdentML. The netCDF reading code has+previously been used in XCMS.")+ (license license:artistic2.0)))+ (define-public r-organismdbi (package (name "r-organismdbi")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex baef88cd2e..a6321a179a 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -8873,67 +8873,6 @@ trait.") proteomics packages.") (license license:artistic2.0))) -(define-public r-mzr- (package- (name "r-mzr")- (version "2.24.1")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "mzR" version))- (sha256- (base32- "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg"))- (modules '((guix build utils)))- (snippet- '(begin- (delete-file-recursively "src/boost")- #t))))- (properties `((upstream-name . "mzR")))- (build-system r-build-system)- (arguments- `(#:phases- (modify-phases %standard-phases- (add-after 'unpack 'use-system-boost- (lambda _- (substitute* "src/Makevars"- (("\\./boost/libs.*") "")- ;; This is to avoid having a plain directory on the list of- ;; libraries to link.- (("\\(RHDF5_LIBS\\)" match)- (string-append match "/libhdf5.a"))- (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")- (("\\ARCH_OBJS=" line)- (string-append line- "\nBOOST_LIBS=-lboost_system -lboost_regex \--lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))- #t)))))- (inputs- `(;; Our default boost package won't work here, unfortunately, even with- ;; mzR version 2.24.1.- ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources- ("zlib" ,zlib)))- (propagated-inputs- `(("r-biobase" ,r-biobase)- ("r-biocgenerics" ,r-biocgenerics)- ("r-ncdf4" ,r-ncdf4)- ("r-protgenerics" ,r-protgenerics)- ("r-rcpp" ,r-rcpp)- ("r-rhdf5lib" ,r-rhdf5lib)- ("r-zlibbioc" ,r-zlibbioc)))- (native-inputs- `(("r-knitr" ,r-knitr)))- (home-page "https://github.com/sneumann/mzR/")- (synopsis "Parser for mass spectrometry data files")- (description- "The mzR package provides a unified API to the common file formats and-parsers available for mass spectrometry data. It comes with a wrapper for the-ISB random access parser for mass spectrometry mzXML, mzData and mzML files.-The package contains the original code written by the ISB, and a subset of the-proteowizard library for mzML and mzIdentML. The netCDF reading code has-previously been used in XCMS.")- (license license:artistic2.0)))- (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2"))-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 34/50] gnu: r-protgenerics: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-34-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-protgenerics): Move from here...* gnu/packages/bioconductor.scm (r-protgenerics): ...to here.--- gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++ gnu/packages/bioinformatics.scm | 20 -------------------- 2 files changed, 20 insertions(+), 20 deletions(-)
Toggle diff (64 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 5ceffd7b4d..a9365a4018 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -3175,6 +3175,26 @@ the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results.") (license license:gpl3+))) +(define-public r-protgenerics+ (package+ (name "r-protgenerics")+ (version "1.22.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "ProtGenerics" version))+ (sha256+ (base32+ "0yihxphgkshvfv1sn67wc4zvr2zlzws2j7ki3zabm6vyfkfdkfiz"))))+ (properties `((upstream-name . "ProtGenerics")))+ (build-system r-build-system)+ (home-page "https://github.com/lgatto/ProtGenerics")+ (synopsis "S4 generic functions for proteomics infrastructure")+ (description+ "This package provides S4 generic functions needed by Bioconductor+proteomics packages.")+ (license license:artistic2.0)))+ (define-public r-rbgl (package (name "r-rbgl")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex a6321a179a..6120cb6804 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -8853,26 +8853,6 @@ for analyzing gene-level association tests in meta-analyses for binary trait.") (license license:gpl3))) -(define-public r-protgenerics- (package- (name "r-protgenerics")- (version "1.22.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "ProtGenerics" version))- (sha256- (base32- "0yihxphgkshvfv1sn67wc4zvr2zlzws2j7ki3zabm6vyfkfdkfiz"))))- (properties `((upstream-name . "ProtGenerics")))- (build-system r-build-system)- (home-page "https://github.com/lgatto/ProtGenerics")- (synopsis "S4 generic functions for proteomics infrastructure")- (description- "This package provides S4 generic functions needed by Bioconductor-proteomics packages.")- (license license:artistic2.0)))- (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2"))-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 35/50] gnu: r-sva: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-35-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-sva): Move from here...* gnu/packages/bioconductor.scm (r-sva): ...to here.--- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-)
Toggle diff (86 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex a9365a4018..a7b1c63b56 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -3524,6 +3524,37 @@ typically represent genomic ranges of interest and the columns represent samples.") (license license:artistic2.0))) +(define-public r-sva+ (package+ (name "r-sva")+ (version "3.38.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "sva" version))+ (sha256+ (base32+ "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy"))))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-edger" ,r-edger)+ ("r-genefilter" ,r-genefilter)+ ("r-mgcv" ,r-mgcv)+ ("r-biocparallel" ,r-biocparallel)+ ("r-matrixstats" ,r-matrixstats)+ ("r-limma" ,r-limma)))+ (home-page "https://bioconductor.org/packages/sva")+ (synopsis "Surrogate variable analysis")+ (description+ "This package contains functions for removing batch effects and other+unwanted variation in high-throughput experiment. It also contains functions+for identifying and building surrogate variables for high-dimensional data+sets. Surrogate variables are covariates constructed directly from+high-dimensional data like gene expression/RNA sequencing/methylation/brain+imaging data that can be used in subsequent analyses to adjust for unknown,+unmodeled, or latent sources of noise.")+ (license license:artistic2.0)))+ (define-public r-systempiper (package (name "r-systempiper")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 6120cb6804..2cc41b7e98 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -8790,37 +8790,6 @@ resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq.") (license license:artistic2.0))) -(define-public r-sva- (package- (name "r-sva")- (version "3.38.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "sva" version))- (sha256- (base32- "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy"))))- (build-system r-build-system)- (propagated-inputs- `(("r-edger" ,r-edger)- ("r-genefilter" ,r-genefilter)- ("r-mgcv" ,r-mgcv)- ("r-biocparallel" ,r-biocparallel)- ("r-matrixstats" ,r-matrixstats)- ("r-limma" ,r-limma)))- (home-page "https://bioconductor.org/packages/sva")- (synopsis "Surrogate variable analysis")- (description- "This package contains functions for removing batch effects and other-unwanted variation in high-throughput experiment. It also contains functions-for identifying and building surrogate variables for high-dimensional data-sets. Surrogate variables are covariates constructed directly from-high-dimensional data like gene expression/RNA sequencing/methylation/brain-imaging data that can be used in subsequent analyses to adjust for unknown,-unmodeled, or latent sources of noise.")- (license license:artistic2.0)))- (define-public r-raremetals2 (package (name "r-raremetals2")-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 36/50] gnu: r-motifrg: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-36-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-motifrg): Move from here...* gnu/packages/bioconductor.scm (r-motifrg): ...to here.--- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-)
Toggle diff (78 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex a7b1c63b56..47a245b4f5 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2924,6 +2924,33 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-motifrg+ (package+ (name "r-motifrg")+ (version "1.31.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "motifRG" version))+ (sha256+ (base32+ "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn"))))+ (properties `((upstream-name . "motifRG")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-biostrings" ,r-biostrings)+ ("r-bsgenome" ,r-bsgenome)+ ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)+ ("r-iranges" ,r-iranges)+ ("r-seqlogo" ,r-seqlogo)+ ("r-xvector" ,r-xvector)))+ (home-page "https://bioconductor.org/packages/motifRG")+ (synopsis "Discover motifs in high throughput sequencing data")+ (description+ "This package provides tools for discriminative motif discovery in high+throughput genetic sequencing data sets using regression methods.")+ (license license:artistic2.0)))+ (define-public r-msnbase (package (name "r-msnbase")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 2cc41b7e98..e2000ccb68 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -7872,33 +7872,6 @@ plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).") (license license:lgpl2.0+))) -(define-public r-motifrg- (package- (name "r-motifrg")- (version "1.31.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "motifRG" version))- (sha256- (base32- "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn"))))- (properties `((upstream-name . "motifRG")))- (build-system r-build-system)- (propagated-inputs- `(("r-biostrings" ,r-biostrings)- ("r-bsgenome" ,r-bsgenome)- ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)- ("r-iranges" ,r-iranges)- ("r-seqlogo" ,r-seqlogo)- ("r-xvector" ,r-xvector)))- (home-page "https://bioconductor.org/packages/motifRG")- (synopsis "Discover motifs in high throughput sequencing data")- (description- "This package provides tools for discriminative motif discovery in high-throughput genetic sequencing data sets using regression methods.")- (license license:artistic2.0)))- (define-public r-zlibbioc (package (name "r-zlibbioc")-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 37/50] gnu: r-seqlogo: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-37-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-seqlogo): Move from here...* gnu/packages/bioconductor.scm (r-seqlogo): ...to here.--- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 23 ----------------------- 2 files changed, 23 insertions(+), 23 deletions(-)
Toggle diff (70 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 47a245b4f5..c58c5af5d6 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -3447,6 +3447,29 @@ differential expression analysis, RNAseq data and related problems.") ;; Any version of the LGPL (license license:lgpl3+))) +(define-public r-seqlogo+ (package+ (name "r-seqlogo")+ (version "1.56.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "seqLogo" version))+ (sha256+ (base32+ "02rpzjjfg5chlwwfbvv72cm78cg2vfmdwzars0cin9hz1hd7rnq1"))))+ (properties `((upstream-name . "seqLogo")))+ (build-system r-build-system)+ (native-inputs+ `(("r-knitr" ,r-knitr)))+ (home-page "https://bioconductor.org/packages/seqLogo")+ (synopsis "Sequence logos for DNA sequence alignments")+ (description+ "seqLogo takes the position weight matrix of a DNA sequence motif and+plots the corresponding sequence logo as introduced by Schneider and+Stephens (1990).")+ (license license:lgpl2.0+)))+ (define-public r-seqpattern (package (name "r-seqpattern")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex e2000ccb68..9ba818d581 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -7849,29 +7849,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-seqlogo- (package- (name "r-seqlogo")- (version "1.56.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "seqLogo" version))- (sha256- (base32- "02rpzjjfg5chlwwfbvv72cm78cg2vfmdwzars0cin9hz1hd7rnq1"))))- (properties `((upstream-name . "seqLogo")))- (build-system r-build-system)- (native-inputs- `(("r-knitr" ,r-knitr)))- (home-page "https://bioconductor.org/packages/seqLogo")- (synopsis "Sequence logos for DNA sequence alignments")- (description- "seqLogo takes the position weight matrix of a DNA sequence motif and-plots the corresponding sequence logo as introduced by Schneider and-Stephens (1990).")- (license license:lgpl2.0+)))- (define-public r-zlibbioc (package (name "r-zlibbioc")-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 38/50] gnu: r-zlibbioc: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-38-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-zlibbioc): Move from here...* gnu/packages/bioconductor.scm (r-zlibbioc): ...to here.--- gnu/packages/bioconductor.scm | 19 +++++++++++++++++++ gnu/packages/bioinformatics.scm | 19 ------------------- 2 files changed, 19 insertions(+), 19 deletions(-)
Toggle diff (62 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex c58c5af5d6..e720d7bf6a 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -3802,6 +3802,25 @@ and specific in detecting differential transcription.") \"externally\" (behind an R external pointer, or on disk).") (license license:artistic2.0))) + (define-public r-zlibbioc+ (package+ (name "r-zlibbioc")+ (version "1.36.0")+ (source (origin+ (method url-fetch)+ (uri (bioconductor-uri "zlibbioc" version))+ (sha256+ (base32+ "0m36ddss0znvm19dhnxcclxjhgjplw8ajk8v419h20ab8an6khxg"))))+ (properties+ `((upstream-name . "zlibbioc")))+ (build-system r-build-system)+ (home-page "https://bioconductor.org/packages/zlibbioc")+ (synopsis "Provider for zlib-1.2.5 to R packages")+ (description "This package uses the source code of zlib-1.2.5 to create+libraries for systems that do not have these available via other means.")+ (license license:artistic2.0)))+ (define-public r-geneplotter (package (name "r-geneplotter")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 9ba818d581..39c437f4a2 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -7849,25 +7849,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-zlibbioc- (package- (name "r-zlibbioc")- (version "1.36.0")- (source (origin- (method url-fetch)- (uri (bioconductor-uri "zlibbioc" version))- (sha256- (base32- "0m36ddss0znvm19dhnxcclxjhgjplw8ajk8v419h20ab8an6khxg"))))- (properties- `((upstream-name . "zlibbioc")))- (build-system r-build-system)- (home-page "https://bioconductor.org/packages/zlibbioc")- (synopsis "Provider for zlib-1.2.5 to R packages")- (description "This package uses the source code of zlib-1.2.5 to create-libraries for systems that do not have these available via other means.")- (license license:artistic2.0)))- (define-public r-r4rna (package (name "r-r4rna")-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 29/50] gnu: r-affyio: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-29-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-affyio): Move from here...* gnu/packages/bioconductor.scm (r-affyio): ...to here.--- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 24 ------------------------ 2 files changed, 24 insertions(+), 24 deletions(-)
Toggle diff (72 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex c63d39dc9c..d0ebcf8481 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -1694,6 +1694,30 @@ problems in CEL-level data to help evaluate performance of quality metrics.") to streamline the more common analyses that a Biostatistician might see.") (license license:artistic2.0))) +(define-public r-affyio+ (package+ (name "r-affyio")+ (version "1.60.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "affyio" version))+ (sha256+ (base32+ "14xnzrxrvgxgixjhq5a9fdgcmrxam2j74hwidkc9if92ffv6s83h"))))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-zlibbioc" ,r-zlibbioc)))+ (inputs+ `(("zlib" ,zlib)))+ (home-page "https://github.com/bmbolstad/affyio")+ (synopsis "Tools for parsing Affymetrix data files")+ (description+ "This package provides routines for parsing Affymetrix data files based+upon file format information. The primary focus is on accessing the CEL and+CDF file formats.")+ (license license:lgpl2.0+)))+ (define-public r-affxparser (package (name "r-affxparser")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 1c90700c95..7256df3f83 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -8934,30 +8934,6 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.") (license license:artistic2.0))) -(define-public r-affyio- (package- (name "r-affyio")- (version "1.60.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "affyio" version))- (sha256- (base32- "14xnzrxrvgxgixjhq5a9fdgcmrxam2j74hwidkc9if92ffv6s83h"))))- (build-system r-build-system)- (propagated-inputs- `(("r-zlibbioc" ,r-zlibbioc)))- (inputs- `(("zlib" ,zlib)))- (home-page "https://github.com/bmbolstad/affyio")- (synopsis "Tools for parsing Affymetrix data files")- (description- "This package provides routines for parsing Affymetrix data files based-upon file format information. The primary focus is on accessing the CEL and-CDF file formats.")- (license license:lgpl2.0+)))- (define-public r-vsn (package (name "r-vsn")-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 41/50] gnu: r-rcas: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-41-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-rcas): Move from here...* gnu/packages/bioconductor.scm (r-rcas): ...to here.--- gnu/packages/bioconductor.scm | 49 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 49 --------------------------------- 2 files changed, 49 insertions(+), 49 deletions(-)
Toggle diff (122 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 99607ba564..1d38fa1c05 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -3307,6 +3307,55 @@ proteomics packages.") the graph algorithms contained in the Boost library.") (license license:artistic2.0))) +(define-public r-rcas+ (package+ (name "r-rcas")+ (version "1.16.0")+ (source (origin+ (method url-fetch)+ (uri (bioconductor-uri "RCAS" version))+ (sha256+ (base32+ "0vdxml618vqvf8xyh0zxs307p9zby0cj9dqyiiz625ilyq1hkw2m"))))+ (properties `((upstream-name . "RCAS")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-biocgenerics" ,r-biocgenerics)+ ("r-biostrings" ,r-biostrings)+ ("r-bsgenome" ,r-bsgenome)+ ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)+ ("r-cowplot" ,r-cowplot)+ ("r-data-table" ,r-data-table)+ ("r-dt" ,r-dt)+ ("r-genomation" ,r-genomation)+ ("r-genomeinfodb" ,r-genomeinfodb)+ ("r-genomicfeatures" ,r-genomicfeatures)+ ("r-genomicranges" ,r-genomicranges)+ ("r-ggplot2" ,r-ggplot2)+ ("r-ggseqlogo" ,r-ggseqlogo)+ ("r-gprofiler2" ,r-gprofiler2)+ ("r-iranges" ,r-iranges)+ ("r-pbapply" ,r-pbapply)+ ("r-pheatmap" ,r-pheatmap)+ ("r-plotly" ,r-plotly)+ ("r-plotrix" ,r-plotrix)+ ("r-proxy" ,r-proxy)+ ("r-ranger" ,r-ranger)+ ("r-rsqlite" ,r-rsqlite)+ ("r-rtracklayer" ,r-rtracklayer)+ ("r-rmarkdown" ,r-rmarkdown)+ ("r-s4vectors" ,r-s4vectors)+ ("pandoc" ,pandoc)))+ (native-inputs+ `(("r-knitr" ,r-knitr)))+ (synopsis "RNA-centric annotation system")+ (description+ "RCAS aims to be a standalone RNA-centric annotation system that provides+intuitive reports and publication-ready graphics. This package provides the R+library implementing most of the pipeline's features.")+ (home-page "https://github.com/BIMSBbioinfo/RCAS")+ (license license:artistic2.0)))+ (define-public r-regioner (package (name "r-regioner")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex ae61ecae74..a1ee4b6772 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -7872,55 +7872,6 @@ including VCF header and contents in RDF and JSON.") secondary structure and comparative analysis in R.") (license license:gpl3+))) -(define-public r-rcas- (package- (name "r-rcas")- (version "1.16.0")- (source (origin- (method url-fetch)- (uri (bioconductor-uri "RCAS" version))- (sha256- (base32- "0vdxml618vqvf8xyh0zxs307p9zby0cj9dqyiiz625ilyq1hkw2m"))))- (properties `((upstream-name . "RCAS")))- (build-system r-build-system)- (propagated-inputs- `(("r-biocgenerics" ,r-biocgenerics)- ("r-biostrings" ,r-biostrings)- ("r-bsgenome" ,r-bsgenome)- ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)- ("r-cowplot" ,r-cowplot)- ("r-data-table" ,r-data-table)- ("r-dt" ,r-dt)- ("r-genomation" ,r-genomation)- ("r-genomeinfodb" ,r-genomeinfodb)- ("r-genomicfeatures" ,r-genomicfeatures)- ("r-genomicranges" ,r-genomicranges)- ("r-ggplot2" ,r-ggplot2)- ("r-ggseqlogo" ,r-ggseqlogo)- ("r-gprofiler2" ,r-gprofiler2)- ("r-iranges" ,r-iranges)- ("r-pbapply" ,r-pbapply)- ("r-pheatmap" ,r-pheatmap)- ("r-plotly" ,r-plotly)- ("r-plotrix" ,r-plotrix)- ("r-proxy" ,r-proxy)- ("r-ranger" ,r-ranger)- ("r-rsqlite" ,r-rsqlite)- ("r-rtracklayer" ,r-rtracklayer)- ("r-rmarkdown" ,r-rmarkdown)- ("r-s4vectors" ,r-s4vectors)- ("pandoc" ,pandoc)))- (native-inputs- `(("r-knitr" ,r-knitr)))- (synopsis "RNA-centric annotation system")- (description- "RCAS aims to be a standalone RNA-centric annotation system that provides-intuitive reports and publication-ready graphics. This package provides the R-library implementing most of the pipeline's features.")- (home-page "https://github.com/BIMSBbioinfo/RCAS")- (license license:artistic2.0)))- (define-public rcas-web (package (name "rcas-web")-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 42/50] gnu: r-mutationalpatterns: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-42-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Move from here...* gnu/packages/bioconductor.scm (r-mutationalpatterns): ...to here.--- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 45 --------------------------------- 2 files changed, 45 insertions(+), 45 deletions(-)
Toggle diff (114 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 1d38fa1c05..7c471c7375 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -3013,6 +3013,51 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") throughput genetic sequencing data sets using regression methods.") (license license:artistic2.0))) +(define-public r-mutationalpatterns+ (package+ (name "r-mutationalpatterns")+ (version "3.0.1")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "MutationalPatterns" version))+ (sha256+ (base32+ "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35"))))+ (build-system r-build-system)+ (native-inputs+ `(("r-knitr" ,r-knitr)))+ (propagated-inputs+ `(("r-biocgenerics" ,r-biocgenerics)+ ("r-biostrings" ,r-biostrings)+ ("r-bsgenome" ,r-bsgenome)+ ;; These two packages are suggested packages+ ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)+ ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)+ ("r-cowplot" ,r-cowplot)+ ("r-dplyr" ,r-dplyr)+ ("r-genomeinfodb" ,r-genomeinfodb)+ ("r-genomicranges" ,r-genomicranges)+ ("r-ggalluvial" ,r-ggalluvial)+ ("r-ggdendro" ,r-ggdendro)+ ("r-ggplot2" ,r-ggplot2)+ ("r-iranges" ,r-iranges)+ ("r-magrittr" ,r-magrittr)+ ("r-nmf" ,r-nmf)+ ("r-pracma" ,r-pracma)+ ("r-purrr" ,r-purrr)+ ("r-s4vectors" ,r-s4vectors)+ ("r-stringr" ,r-stringr)+ ("r-tibble" ,r-tibble)+ ("r-tidyr" ,r-tidyr)+ ("r-variantannotation" ,r-variantannotation)))+ (home-page "https://bioconductor.org/packages/MutationalPatterns/")+ (synopsis "Extract and visualize mutational patterns in genomic data")+ (description "This package provides an extensive toolset for the+characterization and visualization of a wide range of mutational patterns+in SNV base substitution data.")+ (license license:expat)))+ (define-public r-msnbase (package (name "r-msnbase")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex a1ee4b6772..b5b2cc2f6b 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -7923,51 +7923,6 @@ secondary structure and comparative analysis in R.") @dfn{RNA-centric annotation system} (RCAS).") (license license:agpl3+))) -(define-public r-mutationalpatterns- (package- (name "r-mutationalpatterns")- (version "3.0.1")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "MutationalPatterns" version))- (sha256- (base32- "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35"))))- (build-system r-build-system)- (native-inputs- `(("r-knitr" ,r-knitr)))- (propagated-inputs- `(("r-biocgenerics" ,r-biocgenerics)- ("r-biostrings" ,r-biostrings)- ("r-bsgenome" ,r-bsgenome)- ;; These two packages are suggested packages- ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)- ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)- ("r-cowplot" ,r-cowplot)- ("r-dplyr" ,r-dplyr)- ("r-genomeinfodb" ,r-genomeinfodb)- ("r-genomicranges" ,r-genomicranges)- ("r-ggalluvial" ,r-ggalluvial)- ("r-ggdendro" ,r-ggdendro)- ("r-ggplot2" ,r-ggplot2)- ("r-iranges" ,r-iranges)- ("r-magrittr" ,r-magrittr)- ("r-nmf" ,r-nmf)- ("r-pracma" ,r-pracma)- ("r-purrr" ,r-purrr)- ("r-s4vectors" ,r-s4vectors)- ("r-stringr" ,r-stringr)- ("r-tibble" ,r-tibble)- ("r-tidyr" ,r-tidyr)- ("r-variantannotation" ,r-variantannotation)))- (home-page "https://bioconductor.org/packages/MutationalPatterns/")- (synopsis "Extract and visualize mutational patterns in genomic data")- (description "This package provides an extensive toolset for the-characterization and visualization of a wide range of mutational patterns-in SNV base substitution data.")- (license license:expat)))- (define-public r-chipkernels (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372") (revision "1"))-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 43/50] gnu: r-tximport: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-43-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-tximport): Move from here...* gnu/packages/bioconductor.scm (r-tximport): ...to here.--- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 24 ------------------------ 2 files changed, 24 insertions(+), 24 deletions(-)
Toggle diff (72 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 7c471c7375..30d4844ae4 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -3848,6 +3848,30 @@ dependencies between GO terms can be implemented and applied.") ;; Any version of the LGPL applies. (license license:lgpl2.1+))) +(define-public r-tximport+ (package+ (name "r-tximport")+ (version "1.18.0")+ (source (origin+ (method url-fetch)+ (uri (bioconductor-uri "tximport" version))+ (sha256+ (base32+ "1nxnlvl4iv2392xa72j0lzy2xnb3vrvyhfrdj9l54znwkrryyq34"))))+ (build-system r-build-system)+ (native-inputs+ `(("r-knitr" ,r-knitr)))+ (home-page "https://bioconductor.org/packages/tximport")+ (synopsis "Import and summarize transcript-level estimates for gene-level analysis")+ (description+ "This package provides tools to import transcript-level abundance,+estimated counts and transcript lengths, and to summarize them into matrices+for use with downstream gene-level analysis packages. Average transcript+length, weighted by sample-specific transcript abundance estimates, is+provided as a matrix which can be used as an offset for different expression+of gene-level counts.")+ (license license:gpl2+)))+ (define-public r-variantannotation (package (name "r-variantannotation")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex b5b2cc2f6b..83d6797809 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -7990,30 +7990,6 @@ bound and non bound genomic regions to accurately identify transcription factors bound at the specific regions.") (license license:gpl2+))) -(define-public r-tximport- (package- (name "r-tximport")- (version "1.18.0")- (source (origin- (method url-fetch)- (uri (bioconductor-uri "tximport" version))- (sha256- (base32- "1nxnlvl4iv2392xa72j0lzy2xnb3vrvyhfrdj9l54znwkrryyq34"))))- (build-system r-build-system)- (native-inputs- `(("r-knitr" ,r-knitr)))- (home-page "https://bioconductor.org/packages/tximport")- (synopsis "Import and summarize transcript-level estimates for gene-level analysis")- (description- "This package provides tools to import transcript-level abundance,-estimated counts and transcript lengths, and to summarize them into matrices-for use with downstream gene-level analysis packages. Average transcript-length, weighted by sample-specific transcript abundance estimates, is-provided as a matrix which can be used as an offset for different expression-of gene-level counts.")- (license license:gpl2+)))- (define-public r-rhdf5filters (package (name "r-rhdf5filters")-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 44/50] gnu: r-rhdf5filters: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-44-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-rhdf5filters): Move from here...* gnu/packages/bioconductor.scm (r-rhdf5filters): ...to here.--- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 26 insertions(+), 26 deletions(-)
Toggle diff (76 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 30d4844ae4..8695f13ed8 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -3482,6 +3482,32 @@ reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) +(define-public r-rhdf5filters+ (package+ (name "r-rhdf5filters")+ (version "1.2.1")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "rhdf5filters" version))+ (sha256+ (base32+ "1bjlgc76vx0z81s8vci9ln1d2s3b157qnm32xs36mnyjk31ivasz"))))+ (properties `((upstream-name . "rhdf5filters")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-rhdf5lib" ,r-rhdf5lib)))+ (inputs+ `(("zlib" ,zlib)))+ (native-inputs+ `(("r-knitr" ,r-knitr)))+ (home-page "https://github.com/grimbough/rhdf5filters")+ (synopsis "HDF5 compression filters")+ (description+ "This package provides a collection of compression filters for use with+HDF5 datasets.")+ (license license:bsd-2)))+ (define-public r-rsamtools (package (name "r-rsamtools")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 83d6797809..2907d65b38 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -7990,32 +7990,6 @@ bound and non bound genomic regions to accurately identify transcription factors bound at the specific regions.") (license license:gpl2+))) -(define-public r-rhdf5filters- (package- (name "r-rhdf5filters")- (version "1.2.1")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "rhdf5filters" version))- (sha256- (base32- "1bjlgc76vx0z81s8vci9ln1d2s3b157qnm32xs36mnyjk31ivasz"))))- (properties `((upstream-name . "rhdf5filters")))- (build-system r-build-system)- (propagated-inputs- `(("r-rhdf5lib" ,r-rhdf5lib)))- (inputs- `(("zlib" ,zlib)))- (native-inputs- `(("r-knitr" ,r-knitr)))- (home-page "https://github.com/grimbough/rhdf5filters")- (synopsis "HDF5 compression filters")- (description- "This package provides a collection of compression filters for use with-HDF5 datasets.")- (license license:bsd-2)))- (define-public r-rhdf5 (package (name "r-rhdf5")-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 45/50] gnu: r-annotationfilter: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-45-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-annotationfilter): Move from here...* gnu/packages/bioconductor.scm (r-annotationfilter): ...to here.--- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 26 insertions(+), 26 deletions(-)
Toggle diff (76 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 8695f13ed8..87b879ad94 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -1804,6 +1804,32 @@ microarrays.") annotation data packages using SQLite data storage.") (license license:artistic2.0))) +(define-public r-annotationfilter+ (package+ (name "r-annotationfilter")+ (version "1.14.0")+ (source (origin+ (method url-fetch)+ (uri (bioconductor-uri "AnnotationFilter" version))+ (sha256+ (base32+ "0npk0laa2rc93rsh6yikj886zf2fl53a050j07fj9w67j0q0h3s9"))))+ (properties+ `((upstream-name . "AnnotationFilter")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-genomicranges" ,r-genomicranges)+ ("r-lazyeval" ,r-lazyeval)))+ (native-inputs+ `(("r-knitr" ,r-knitr)))+ (home-page "https://github.com/Bioconductor/AnnotationFilter")+ (synopsis "Facilities for filtering Bioconductor annotation resources")+ (description+ "This package provides classes and other infrastructure to implement+filters for manipulating Bioconductor annotation resources. The filters are+used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")+ (license license:artistic2.0)))+ (define-public r-annotationforge (package (name "r-annotationforge")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 2907d65b38..7ad51d3518 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -8029,32 +8029,6 @@ package, and for letting R applications work on datasets that are larger than the available RAM.") (license license:artistic2.0))) -(define-public r-annotationfilter- (package- (name "r-annotationfilter")- (version "1.14.0")- (source (origin- (method url-fetch)- (uri (bioconductor-uri "AnnotationFilter" version))- (sha256- (base32- "0npk0laa2rc93rsh6yikj886zf2fl53a050j07fj9w67j0q0h3s9"))))- (properties- `((upstream-name . "AnnotationFilter")))- (build-system r-build-system)- (propagated-inputs- `(("r-genomicranges" ,r-genomicranges)- ("r-lazyeval" ,r-lazyeval)))- (native-inputs- `(("r-knitr" ,r-knitr)))- (home-page "https://github.com/Bioconductor/AnnotationFilter")- (synopsis "Facilities for filtering Bioconductor annotation resources")- (description- "This package provides classes and other infrastructure to implement-filters for manipulating Bioconductor annotation resources. The filters are-used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")- (license license:artistic2.0)))- (define-public emboss (package (name "emboss")-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 46/50] gnu: r-rhdf5: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-46-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-rhdf5): Move from here...* gnu/packages/bioconductor.scm (r-rhdf5): ...to here.--- gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 39 --------------------------------- 2 files changed, 39 insertions(+), 39 deletions(-)
Toggle diff (102 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 87b879ad94..d027a24bf3 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -3508,6 +3508,45 @@ reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) +(define-public r-rhdf5+ (package+ (name "r-rhdf5")+ (version "2.34.0")+ (source (origin+ (method url-fetch)+ (uri (bioconductor-uri "rhdf5" version))+ (sha256+ (base32+ "0almr1vscrgj5g4dyrags131wia2pmdbdidlpskbgm44ha6hpmqi"))))+ (build-system r-build-system)+ (arguments+ `(#:phases+ (modify-phases %standard-phases+ (add-after 'unpack 'fix-linking+ (lambda _+ (substitute* "src/Makevars"+ ;; This is to avoid having a plain directory on the list of+ ;; libraries to link.+ (("\\(RHDF5_LIBS\\)" match)+ (string-append match "/libhdf5.a")))+ #t)))))+ (propagated-inputs+ `(("r-rhdf5filters" ,r-rhdf5filters)+ ("r-rhdf5lib" ,r-rhdf5lib)))+ (native-inputs+ `(("r-knitr" ,r-knitr)))+ (home-page "https://bioconductor.org/packages/rhdf5")+ (synopsis "HDF5 interface to R")+ (description+ "This R/Bioconductor package provides an interface between HDF5 and R.+HDF5's main features are the ability to store and access very large and/or+complex datasets and a wide variety of metadata on mass storage (disk) through+a completely portable file format. The rhdf5 package is thus suited for the+exchange of large and/or complex datasets between R and other software+package, and for letting R applications work on datasets that are larger than+the available RAM.")+ (license license:artistic2.0)))+ (define-public r-rhdf5filters (package (name "r-rhdf5filters")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 7ad51d3518..ef0d7b3007 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -7990,45 +7990,6 @@ bound and non bound genomic regions to accurately identify transcription factors bound at the specific regions.") (license license:gpl2+))) -(define-public r-rhdf5- (package- (name "r-rhdf5")- (version "2.34.0")- (source (origin- (method url-fetch)- (uri (bioconductor-uri "rhdf5" version))- (sha256- (base32- "0almr1vscrgj5g4dyrags131wia2pmdbdidlpskbgm44ha6hpmqi"))))- (build-system r-build-system)- (arguments- `(#:phases- (modify-phases %standard-phases- (add-after 'unpack 'fix-linking- (lambda _- (substitute* "src/Makevars"- ;; This is to avoid having a plain directory on the list of- ;; libraries to link.- (("\\(RHDF5_LIBS\\)" match)- (string-append match "/libhdf5.a")))- #t)))))- (propagated-inputs- `(("r-rhdf5filters" ,r-rhdf5filters)- ("r-rhdf5lib" ,r-rhdf5lib)))- (native-inputs- `(("r-knitr" ,r-knitr)))- (home-page "https://bioconductor.org/packages/rhdf5")- (synopsis "HDF5 interface to R")- (description- "This R/Bioconductor package provides an interface between HDF5 and R.-HDF5's main features are the ability to store and access very large and/or-complex datasets and a wide variety of metadata on mass storage (disk) through-a completely portable file format. The rhdf5 package is thus suited for the-exchange of large and/or complex datasets between R and other software-package, and for letting R applications work on datasets that are larger than-the available RAM.")- (license license:artistic2.0)))- (define-public emboss (package (name "emboss")-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 47/50] gnu: r-chipseq: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-47-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-chipseq): Move from here...* gnu/packages/bioconductor.scm (r-chipseq): ...to here.--- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 26 insertions(+), 26 deletions(-)
Toggle diff (76 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex d027a24bf3..f224a5ecb4 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2206,6 +2206,32 @@ genome data packages and support for efficient SNP representation.") analysis.") (license license:artistic2.0))) +(define-public r-chipseq+ (package+ (name "r-chipseq")+ (version "1.40.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "chipseq" version))+ (sha256+ (base32+ "12pzq24aarvgxfmhcad0l5g951xqdvvi7bspgbsvlvmfkqd74j2v"))))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-biocgenerics" ,r-biocgenerics)+ ("r-genomicranges" ,r-genomicranges)+ ("r-iranges" ,r-iranges)+ ("r-lattice" ,r-lattice)+ ("r-s4vectors" ,r-s4vectors)+ ("r-shortread" ,r-shortread)))+ (home-page "https://bioconductor.org/packages/chipseq")+ (synopsis "Package for analyzing ChIPseq data")+ (description+ "This package provides tools for processing short read data from ChIPseq+experiments.")+ (license license:artistic2.0)))+ (define-public r-complexheatmap (package (name "r-complexheatmap")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex ef0d7b3007..3ee3d9d4f3 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -8312,32 +8312,6 @@ analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.") (license license:gpl3+))) -(define-public r-chipseq- (package- (name "r-chipseq")- (version "1.40.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "chipseq" version))- (sha256- (base32- "12pzq24aarvgxfmhcad0l5g951xqdvvi7bspgbsvlvmfkqd74j2v"))))- (build-system r-build-system)- (propagated-inputs- `(("r-biocgenerics" ,r-biocgenerics)- ("r-genomicranges" ,r-genomicranges)- ("r-iranges" ,r-iranges)- ("r-lattice" ,r-lattice)- ("r-s4vectors" ,r-s4vectors)- ("r-shortread" ,r-shortread)))- (home-page "https://bioconductor.org/packages/chipseq")- (synopsis "Package for analyzing ChIPseq data")- (description- "This package provides tools for processing short read data from ChIPseq-experiments.")- (license license:artistic2.0)))- (define-public r-copyhelper (package (name "r-copyhelper")-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 48/50] gnu: r-copyhelper: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-48-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-copyhelper): Move from here...* gnu/packages/bioconductor.scm (r-copyhelper): ...to here.[source]: Repalce 'string-append' by 'bioconductor-uri' with 'experiment.--- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 24 insertions(+), 26 deletions(-)
Toggle diff (74 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex f224a5ecb4..eee1561c1b 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -999,6 +999,30 @@ from Illumina 450k methylation arrays.") chromstaR package.") (license license:gpl3))) +(define-public r-copyhelper+ (package+ (name "r-copyhelper")+ (version "1.6.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "CopyhelpeR" version 'experiment))+ (sha256+ (base32+ "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))+ (properties `((upstream-name . "CopyhelpeR")))+ (build-system r-build-system)+ (home-page "https://bioconductor.org/packages/CopyhelpeR/")+ (synopsis "Helper files for CopywriteR")+ (description+ "This package contains the helper files that are required to run the+Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content+and mappability files for the reference genomes hg18, hg19, hg38, mm9 and+mm10. In addition, it contains a blacklist filter to remove regions that+display copy number variation. Files are stored as GRanges objects from the+GenomicRanges Bioconductor package.")+ (license license:gpl2)))+ (define-public r-genelendatabase (package (name "r-genelendatabase")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 3ee3d9d4f3..2acca0c055 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -8312,32 +8312,6 @@ analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.") (license license:gpl3+))) -(define-public r-copyhelper- (package- (name "r-copyhelper")- (version "1.6.0")- (source- (origin- (method url-fetch)- (uri (string-append "https://bioconductor.org/packages/release/"- "data/experiment/src/contrib/CopyhelpeR_"- version ".tar.gz"))- (sha256- (base32- "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))- (properties `((upstream-name . "CopyhelpeR")))- (build-system r-build-system)- (home-page "https://bioconductor.org/packages/CopyhelpeR/")- (synopsis "Helper files for CopywriteR")- (description- "This package contains the helper files that are required to run the-Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content-and mappability files for the reference genomes hg18, hg19, hg38, mm9 and-mm10. In addition, it contains a blacklist filter to remove regions that-display copy number variation. Files are stored as GRanges objects from the-GenomicRanges Bioconductor package.")- (license license:gpl2)))- (define-public r-copywriter (package (name "r-copywriter")-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 50/50] gnu: r-methylkit: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-50-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-methylkit): Move from here...* gnu/packages/bioconductor.scm (r-methylkit): ...to here.--- gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 47 --------------------------------- 2 files changed, 47 insertions(+), 47 deletions(-)
Toggle diff (118 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex fe91fd486f..54a6afcf3d 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -3102,6 +3102,53 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-methylkit+ (package+ (name "r-methylkit")+ (version "1.16.1")+ (source (origin+ (method url-fetch)+ (uri (bioconductor-uri "methylKit" version))+ (sha256+ (base32+ "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3"))))+ (properties `((upstream-name . "methylKit")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-data-table" ,r-data-table)+ ("r-emdbook" ,r-emdbook)+ ("r-fastseg" ,r-fastseg)+ ("r-genomeinfodb" ,r-genomeinfodb)+ ("r-genomicranges" ,r-genomicranges)+ ("r-gtools" ,r-gtools)+ ("r-iranges" ,r-iranges)+ ("r-kernsmooth" ,r-kernsmooth)+ ("r-limma" ,r-limma)+ ("r-mclust" ,r-mclust)+ ("r-mgcv" ,r-mgcv)+ ("r-qvalue" ,r-qvalue)+ ("r-r-utils" ,r-r-utils)+ ("r-rcpp" ,r-rcpp)+ ("r-rhtslib" ,r-rhtslib)+ ("r-rsamtools" ,r-rsamtools)+ ("r-rtracklayer" ,r-rtracklayer)+ ("r-s4vectors" ,r-s4vectors)+ ("r-zlibbioc" ,r-zlibbioc)))+ (native-inputs+ `(("r-knitr" ,r-knitr))) ; for vignettes+ (home-page "https://github.com/al2na/methylKit")+ (synopsis+ "DNA methylation analysis from high-throughput bisulfite sequencing results")+ (description+ "MethylKit is an R package for DNA methylation analysis and annotation+from high-throughput bisulfite sequencing. The package is designed to deal+with sequencing data from @dfn{Reduced representation bisulfite+sequencing} (RRBS) and its variants, but also target-capture methods and whole+genome bisulfite sequencing. It also has functions to analyze base-pair+resolution 5hmC data from experimental protocols such as oxBS-Seq and+TAB-Seq.")+ (license license:artistic2.0)))+ (define-public r-motifrg (package (name "r-motifrg")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 79146f915f..48b521f755 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -8312,53 +8312,6 @@ analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.") (license license:gpl3+))) -(define-public r-methylkit- (package- (name "r-methylkit")- (version "1.16.1")- (source (origin- (method url-fetch)- (uri (bioconductor-uri "methylKit" version))- (sha256- (base32- "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3"))))- (properties `((upstream-name . "methylKit")))- (build-system r-build-system)- (propagated-inputs- `(("r-data-table" ,r-data-table)- ("r-emdbook" ,r-emdbook)- ("r-fastseg" ,r-fastseg)- ("r-genomeinfodb" ,r-genomeinfodb)- ("r-genomicranges" ,r-genomicranges)- ("r-gtools" ,r-gtools)- ("r-iranges" ,r-iranges)- ("r-kernsmooth" ,r-kernsmooth)- ("r-limma" ,r-limma)- ("r-mclust" ,r-mclust)- ("r-mgcv" ,r-mgcv)- ("r-qvalue" ,r-qvalue)- ("r-r-utils" ,r-r-utils)- ("r-rcpp" ,r-rcpp)- ("r-rhtslib" ,r-rhtslib)- ("r-rsamtools" ,r-rsamtools)- ("r-rtracklayer" ,r-rtracklayer)- ("r-s4vectors" ,r-s4vectors)- ("r-zlibbioc" ,r-zlibbioc)))- (native-inputs- `(("r-knitr" ,r-knitr))) ; for vignettes- (home-page "https://github.com/al2na/methylKit")- (synopsis- "DNA methylation analysis from high-throughput bisulfite sequencing results")- (description- "MethylKit is an R package for DNA methylation analysis and annotation-from high-throughput bisulfite sequencing. The package is designed to deal-with sequencing data from @dfn{Reduced representation bisulfite-sequencing} (RRBS) and its variants, but also target-capture methods and whole-genome bisulfite sequencing. It also has functions to analyze base-pair-resolution 5hmC data from experimental protocols such as oxBS-Seq and-TAB-Seq.")- (license license:artistic2.0)))- (define-public r-raremetals2 (package (name "r-raremetals2")-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 49/50] gnu: r-copywriter: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-49-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-copywriter): Move from here...* gnu/packages/bioconductor.scm (r-copywriter): ...to here.--- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 40 --------------------------------- 2 files changed, 40 insertions(+), 40 deletions(-)
Toggle diff (104 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex eee1561c1b..fe91fd486f 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -2295,6 +2295,46 @@ provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation graphics.") (license license:gpl2+))) +(define-public r-copywriter+ (package+ (name "r-copywriter")+ (version "2.22.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "CopywriteR" version))+ (sha256+ (base32+ "060p6l6l8i6b15hyyz5v5kkxih3h4wcciixii51m9mn82z23xr2f"))))+ (properties `((upstream-name . "CopywriteR")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-biocparallel" ,r-biocparallel)+ ("r-chipseq" ,r-chipseq)+ ("r-copyhelper" ,r-copyhelper)+ ("r-data-table" ,r-data-table)+ ("r-dnacopy" ,r-dnacopy)+ ("r-futile-logger" ,r-futile-logger)+ ("r-genomeinfodb" ,r-genomeinfodb)+ ("r-genomicalignments" ,r-genomicalignments)+ ("r-genomicranges" ,r-genomicranges)+ ("r-gtools" ,r-gtools)+ ("r-iranges" ,r-iranges)+ ("r-matrixstats" ,r-matrixstats)+ ("r-rsamtools" ,r-rsamtools)+ ("r-s4vectors" ,r-s4vectors)))+ (home-page "https://github.com/PeeperLab/CopywriteR")+ (synopsis "Copy number information from targeted sequencing")+ (description+ "CopywriteR extracts DNA copy number information from targeted sequencing+by utilizing off-target reads. It allows for extracting uniformly distributed+copy number information, can be used without reference, and can be applied to+sequencing data obtained from various techniques including chromatin+immunoprecipitation and target enrichment on small gene panels. Thereby,+CopywriteR constitutes a widely applicable alternative to available copy+number detection tools.")+ (license license:gpl2)))+ (define-public r-deseq (package (name "r-deseq")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 2acca0c055..79146f915f 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -8312,46 +8312,6 @@ analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.") (license license:gpl3+))) -(define-public r-copywriter- (package- (name "r-copywriter")- (version "2.22.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "CopywriteR" version))- (sha256- (base32- "060p6l6l8i6b15hyyz5v5kkxih3h4wcciixii51m9mn82z23xr2f"))))- (properties `((upstream-name . "CopywriteR")))- (build-system r-build-system)- (propagated-inputs- `(("r-biocparallel" ,r-biocparallel)- ("r-chipseq" ,r-chipseq)- ("r-copyhelper" ,r-copyhelper)- ("r-data-table" ,r-data-table)- ("r-dnacopy" ,r-dnacopy)- ("r-futile-logger" ,r-futile-logger)- ("r-genomeinfodb" ,r-genomeinfodb)- ("r-genomicalignments" ,r-genomicalignments)- ("r-genomicranges" ,r-genomicranges)- ("r-gtools" ,r-gtools)- ("r-iranges" ,r-iranges)- ("r-matrixstats" ,r-matrixstats)- ("r-rsamtools" ,r-rsamtools)- ("r-s4vectors" ,r-s4vectors)))- (home-page "https://github.com/PeeperLab/CopywriteR")- (synopsis "Copy number information from targeted sequencing")- (description- "CopywriteR extracts DNA copy number information from targeted sequencing-by utilizing off-target reads. It allows for extracting uniformly distributed-copy number information, can be used without reference, and can be applied to-sequencing data obtained from various techniques including chromatin-immunoprecipitation and target enrichment on small gene panels. Thereby,-CopywriteR constitutes a widely applicable alternative to available copy-number detection tools.")- (license license:gpl2)))- (define-public r-methylkit (package (name "r-methylkit")-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 39/50] gnu: r-rhtslib: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-39-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-rhtslib): Move from here...* gnu/packages/bioconductor.scm (r-rhtslib): ...to here.--- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 32 insertions(+), 31 deletions(-)
Toggle diff (94 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex e720d7bf6a..8e78a2a0ca 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -39,6 +39,7 @@ #:use-module (gnu packages boost) #:use-module (gnu packages cran) #:use-module (gnu packages compression)+ #:use-module (gnu packages curl) #:use-module (gnu packages gcc) #:use-module (gnu packages graph) #:use-module (gnu packages graphviz)@@ -2832,6 +2833,37 @@ Enrichment Analysis} (GSEA).") the Human Protein Atlas project.") (license license:artistic2.0))) +(define-public r-rhtslib+ (package+ (name "r-rhtslib")+ (version "1.22.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "Rhtslib" version))+ (sha256+ (base32+ "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4"))))+ (properties `((upstream-name . "Rhtslib")))+ (build-system r-build-system)+ ;; Without this a temporary directory ends up in the Rhtslib.so binary,+ ;; which makes R abort the build.+ (arguments '(#:configure-flags '("--no-staged-install")))+ (propagated-inputs+ `(("curl" ,curl)+ ("zlib" ,zlib) ; packages using rhtslib need to link with zlib+ ("r-zlibbioc" ,r-zlibbioc)))+ (native-inputs+ `(("pkg-config" ,pkg-config)+ ("r-knitr" ,r-knitr)))+ (home-page "https://github.com/nhayden/Rhtslib")+ (synopsis "High-throughput sequencing library as an R package")+ (description+ "This package provides the HTSlib C library for high-throughput+nucleotide sequence analysis. The package is primarily useful to developers+of other R packages who wish to make use of HTSlib.")+ (license license:lgpl2.0+)))+ (define-public r-impute (package (name "r-impute")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 39c437f4a2..586efcf21e 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -7872,37 +7872,6 @@ including VCF header and contents in RDF and JSON.") secondary structure and comparative analysis in R.") (license license:gpl3+))) -(define-public r-rhtslib- (package- (name "r-rhtslib")- (version "1.22.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "Rhtslib" version))- (sha256- (base32- "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4"))))- (properties `((upstream-name . "Rhtslib")))- (build-system r-build-system)- ;; Without this a temporary directory ends up in the Rhtslib.so binary,- ;; which makes R abort the build.- (arguments '(#:configure-flags '("--no-staged-install")))- (propagated-inputs- `(("curl" ,curl)- ("zlib" ,zlib) ; packages using rhtslib need to link with zlib- ("r-zlibbioc" ,r-zlibbioc)))- (native-inputs- `(("pkg-config" ,pkg-config)- ("r-knitr" ,r-knitr)))- (home-page "https://github.com/nhayden/Rhtslib")- (synopsis "High-throughput sequencing library as an R package")- (description- "This package provides the HTSlib C library for high-throughput-nucleotide sequence analysis. The package is primarily useful to developers-of other R packages who wish to make use of HTSlib.")- (license license:lgpl2.0+)))- (define-public r-bamsignals (package (name "r-bamsignals")-- 2.30.1
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zimoun wrote on 21 May 22:26 +0200
[PATCH 40/50] gnu: r-bamsignals: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)
20210521202622.26591-40-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-bamsignals): Move from here...* gnu/packages/bioconductor.scm (r-bamsignals): ...to here.--- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-)
Toggle diff (84 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 8e78a2a0ca..99607ba564 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -1904,6 +1904,36 @@ standalone, be utilized in other packages, or be wrapped up in higher-level classes.") (license license:gpl2+))) +(define-public r-bamsignals+ (package+ (name "r-bamsignals")+ (version "1.22.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "bamsignals" version))+ (sha256+ (base32+ "0p3r9z9z5sfkd0b951cgr751k4z0yviyn1jfw9d4fcnyld7g1jxv"))))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-biocgenerics" ,r-biocgenerics)+ ("r-genomicranges" ,r-genomicranges)+ ("r-iranges" ,r-iranges)+ ("r-rcpp" ,r-rcpp)+ ("r-rhtslib" ,r-rhtslib)+ ("r-zlibbioc" ,r-zlibbioc)))+ (native-inputs+ `(("r-knitr" ,r-knitr)))+ (home-page "https://bioconductor.org/packages/bamsignals")+ (synopsis "Extract read count signals from bam files")+ (description+ "This package efficiently obtains count vectors from indexed bam+files. It counts the number of nucleotide sequence reads in given genomic+ranges and it computes reads profiles and coverage profiles. It also handles+paired-end data.")+ (license license:gpl2+)))+ (define-public r-biobase (package (name "r-biobase")diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 586efcf21e..ae61ecae74 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -7872,36 +7872,6 @@ including VCF header and contents in RDF and JSON.") secondary structure and comparative analysis in R.") (license license:gpl3+))) -(define-public r-bamsignals- (package- (name "r-bamsignals")- (version "1.22.0")- (source- (origin- (method url-fetch)- (uri (bioconductor-uri "bamsignals" version))- (sha256- (base32- "0p3r9z9z5sfkd0b951cgr751k4z0yviyn1jfw9d4fcnyld7g1jxv"))))- (build-system r-build-system)- (propagated-inputs- `(("r-biocgenerics" ,r-biocgenerics)- ("r-genomicranges" ,r-genomicranges)- ("r-iranges" ,r-iranges)- ("r-rcpp" ,r-rcpp)- ("r-rhtslib" ,r-rhtslib)- ("r-zlibbioc" ,r-zlibbioc)))- (native-inputs- `(("r-knitr" ,r-knitr)))- (home-page "https://bioconductor.org/packages/bamsignals")- (synopsis "Extract read count signals from bam files")- (description- "This package efficiently obtains count vectors from indexed bam-files. It counts the number of nucleotide sequence reads in given genomic-ranges and it computes reads profiles and coverage profiles. It also handles-paired-end data.")- (license license:gpl2+)))- (define-public r-rcas (package (name "r-rcas")-- 2.30.1
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Ricardo Wurmus wrote on 31 May 16:07 +0200
[PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor).
(address . 48575-done@debbugs.gnu.org)
87o8crvvwk.fsf@elephly.net
Thank you for working on this!I have just applied these patches.
-- Ricardo
Closed
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