gnu: Add r-anota2seq, r-hybridmtest, r-apalyzer, r-org-sc-sgd-db, r-apcomplex, r-mdqc, , r-parody, r-arraymvout, r-arrayquality, r-beaddatapackr, r-beadarray, r-arrayqualitymetrics, r-repmis, r-setrng..

  • Done
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3 participants
  • M?d?lin Ionel Patra?cu
  • Bruno Victal
  • Ricardo Wurmus
Owner
unassigned
Submitted by
M?d?lin Ionel Patra?cu
Severity
normal
M
M
M?d?lin Ionel Patra?cu wrote on 24 Mar 2023 23:25
(address . guix-patches@gnu.org)
4619c49d-2e96-49a5-7bf1-81877eb94696@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-anota2seq, r-hybridmtest, r-apalyzer,
r-org-sc-sgd-db, r-apcomplex, r-mdqc,
r-parody, r-arraymvout, r-arrayquality, r-beaddatapackr, r-beadarray,
r-arrayqualitymetrics): New variables.

* gnu/packages/cran.scm (r-repmis, r-setrng): New variables.

--
System Administrator
Bioinformatics and Omics Data Science
BIMSB - MDC
M
M
M?d?lin Ionel Patra?cu wrote on 25 Mar 2023 00:18
20230324231900.28367-4-madalinionel.patrascu@mdc-berlin.de
Date: Fri, 24 Mar 2023 00:51:48 +0100
Subject: [PATCH 04/14] gnu: Add r-apalyzer.

* gnu/packages/bioconductor.scm (r-apalyzer): New variable.
---
gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++
1 file changed, 45 insertions(+)

Toggle diff (58 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c58613bea3..3ae0dba919 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9354,6 +9354,51 @@ (define r-rcppnumerical
@code{Rcpp}.")
(license license:gpl2+)))
+(define-public r-apalyzer
+ (package
+ (name "r-apalyzer")
+ (version "1.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "APAlyzer" version))
+ (sha256
+ (base32 "1iaz9ircfh5x3z5pibn5vnd4lbbr7m5ypk97xnizn22z41aqrxn3"))))
+ (properties `((upstream-name . "APAlyzer")))
+ (build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'install 'change-home-dir
+ (lambda _
+ ;; Change from /homeless-shelter to /tmp for write permission.
+ (setenv "HOME" "/tmp"))))))
+ (propagated-inputs
+ (list r-deseq2
+ r-dplyr
+ r-genomicalignments
+ r-genomicfeatures
+ r-genomicranges
+ r-ggplot2
+ r-ggrepel
+ r-hybridmtest
+ r-repmis
+ r-rsamtools
+ r-rsubread
+ r-rtracklayer
+ r-summarizedexperiment
+ r-tidyr
+ r-variantannotation))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/RJWANGbioinfo/APAlyzer/")
+ (synopsis "Toolkit for APA analysis using RNA-seq data")
+ (description
+ "The APAlyzer package performs @acronym{3'UTR, Three Prime Untranslated
+Region} @acronym{APA, Alternative polyadenylation}, Intronic APA and gene
+expression analysis using RNA-seq data.")
+ (license license:lgpl3)))
+
(define-public r-apeglm
(package
(name "r-apeglm")
--
2.39.2
M
M
M?d?lin Ionel Patra?cu wrote on 25 Mar 2023 00:18
20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-anota2seq): New variable.
---
gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++++
1 file changed, 36 insertions(+)

Toggle diff (51 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fe446df67a..37b649a7d6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12069,6 +12069,42 @@ (define-public r-anota
the data set is suitable for such analysis.")
(license license:gpl3)))
+(define-public r-anota2seq
+ (package
+ (name "r-anota2seq")
+ (version "1.20.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "anota2seq" version))
+ (sha256
+ (base32 "14ggggfa6mdqcb2hfvann9mb66s7a9nxlnh31zblb3mrrjizg1x3"))))
+ (properties `((upstream-name . "anota2seq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-deseq2
+ r-edger
+ r-limma
+ r-multtest
+ r-qvalue
+ r-rcolorbrewer
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/anota2seq")
+ (synopsis "Transcriptome-wide analysis of translational efficiency")
+ (description
+ "The anota2seq package provides analysis of translational efficiency and
+differential expression analysis for polysome-profiling and ribosome-profiling
+studies (two or more sample classes) quantified by RNA sequencing or
+DNA-microarray. Polysome-profiling and ribosome-profiling typically generate
+data for two RNA sources, translated mRNA and total mRNA. Analysis of
+differential expression is used to estimate changes within each RNA source.
+Analysis of translational efficiency aims to identify changes in translation
+efficiency leading to altered protein levels that are independent of total mRNA
+levels or buffering, a mechanism regulating translational efficiency so that
+protein levels remain constant despite fluctuating total mRNA levels.")
+ (license license:gpl3)))
+
(define-public r-sigpathway
(package
(name "r-sigpathway")

base-commit: ef71e3290916583973724316e815cee840c1b6d8
--
2.39.2
M
M
M?d?lin Ionel Patra?cu wrote on 25 Mar 2023 00:18
[PATCH 03/14] gnu: Add r-hybridmtest.
20230324231900.28367-3-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-hybridmtest): New variable.
---
gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)

Toggle diff (43 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 37b649a7d6..c58613bea3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -16248,6 +16248,36 @@ (define-public r-rsbml
validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
(license license:artistic2.0)))
+(define-public r-hybridmtest
+ (package
+ (name "r-hybridmtest")
+ (version "1.42.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "HybridMTest" version))
+ (sha256
+ (base32 "0mv092lq8548l306ghgvh8yka1fnyvs7w1yzfjzcchj8vlsb0qns"))))
+ (properties `((upstream-name . "HybridMTest")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biobase
+ r-fdrtool
+ r-mass
+ r-survival))
+ (home-page "https://bioconductor.org/packages/HybridMTest")
+ (synopsis "Hybrid multiple testing")
+ (description
+ "This package performs hybrid multiple testing that incorporates method
+selection and assumption evaluations into the analysis using @acronym{EBP,
+empirical Bayes probability} estimates obtained by Grenander density estimation.
+For instance, for 3-group comparison analysis, Hybrid Multiple testing considers
+EBPs as weighted EBPs between F-test and H-test with EBPs from Shapiro Wilk test
+of normality as weigth. Instead of just using EBPs from F-test only or using H-
+test only, this methodology combines both types of EBPs through EBPs from Shapiro
+Wilk test of normality. This methodology uses then the law of total EBPs.")
+ (license license:gpl2+)))
+
(define-public r-hypergraph
(package
(name "r-hypergraph")
--
2.39.2
M
M
M?d?lin Ionel Patra?cu wrote on 25 Mar 2023 00:18
[PATCH 05/14] gnu: Add r-org-sc-sgd-db.
20230324231900.28367-5-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-org-sc-sgd-db): New variable.
---
gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++
1 file changed, 21 insertions(+)

Toggle diff (34 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3ae0dba919..21aa3476c0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -116,6 +116,27 @@ (define-public r-org-bt-eg-db
based on mapping using Entrez Gene identifiers.")
(license license:artistic2.0)))
+(define-public r-org-sc-sgd-db
+ (package
+ (name "r-org-sc-sgd-db")
+ (version "3.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "org.Sc.sgd.db" version
+ 'annotation))
+ (sha256
+ (base32 "03b8m4p865kzhjj8zyhmc0ic0n4jyjdl4h8a8xny10b7xs6l0v9f"))))
+ (properties `((upstream-name . "org.Sc.sgd.db")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-annotationdbi))
+ (home-page "https://bioconductor.org/packages/org.Sc.sgd.db")
+ (synopsis "Genome wide annotation for Yeast")
+ (description
+ "Genome wide annotation for Yeast, primarily based on mapping using ORF
+identifiers from @acronym{SGD, Saccharomyces Genome Database}.")
+ (license license:artistic2.0)))
+
(define-public r-pd-mapping50k-xba240
(package
(name "r-pd-mapping50k-xba240")
--
2.39.2
M
M
M?d?lin Ionel Patra?cu wrote on 25 Mar 2023 00:18
[PATCH 02/14] gnu: Add r-repmis.
20230324231900.28367-2-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/cran.scm (r-repmis): New variable.
---
gnu/packages/cran.scm | 34 ++++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)

Toggle diff (47 lines)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a36c845479..325fec402b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2894,6 +2894,40 @@ (define-public r-selectr
package is a port of the Python package @code{cssselect}.")
(license license:bsd-3)))
+(define-public r-repmis
+ (package
+ (name "r-repmis")
+ (version "0.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "repmis" version))
+ (sha256
+ (base32 "0z5mjbsl24yjbl0aawr35grcal44rf2xbwv1hy7bdkms94ix79b5"))))
+ (properties `((upstream-name . "repmis")))
+ (build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'install 'change-home-dir
+ (lambda _
+ ;; Change from /homeless-shelter to /tmp for write permission.
+ (setenv "HOME" "/tmp"))))))
+ (propagated-inputs
+ (list r-data-table
+ r-digest
+ r-httr
+ r-plyr
+ r-r-cache))
+ (home-page "http://cran.r-project.org/package=repmis")
+ (synopsis "Miscellaneous tools for reproducible research")
+ (description
+ "This package is a colletion of tools to load R packages and automatically
+generate BibTeX files citing them as well as load and cache plain-text and Excel
+formatted data stored on GitHub, and from other sources.")
+ (license license:gpl3+)))
+
(define-public r-reprex
(package
(name "r-reprex")
--
2.39.2
M
M
M?d?lin Ionel Patra?cu wrote on 25 Mar 2023 00:18
[PATCH 07/14] gnu: Add r-mdqc.
20230324231900.28367-7-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-mdqc): New variable.
---
gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)

Toggle diff (38 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 71d65d64a5..39367dd927 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6968,6 +6968,31 @@ (define-public r-maser
and visualizaton of alternative splicing events generated by rMATS.")
(license license:expat)))
+(define-public r-mdqc
+ (package
+ (name "r-mdqc")
+ (version "1.60.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "mdqc" version))
+ (sha256
+ (base32 "1hn6m0z8q3jnzb0h8m29khgm0cx81cfs3s1j6hlg4wsrwkha1i3w"))))
+ (properties `((upstream-name . "mdqc")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-cluster
+ r-mass))
+ (home-page "https://bioconductor.org/packages/mdqc")
+ (synopsis "Mahalanobis distance quality control for microarrays")
+ (description
+ "MDQC is a multivariate quality assessment method for microarrays based on
+quality control (QC) reports. The Mahalanobis distance of an array's quality
+attributes is used to measure the similarity of the quality of that array
+against the quality of the other arrays. Then, arrays with unusually high
+distances can be flagged as potentially low-quality.")
+ (license license:lgpl2.0+)))
+
(define-public r-metagenomeseq
(package
(name "r-metagenomeseq")
--
2.39.2
M
M
M?d?lin Ionel Patra?cu wrote on 25 Mar 2023 00:18
[PATCH 06/14] gnu: Add r-apcomplex.
20230324231900.28367-6-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-apcomplex): New variable.
---
gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)

Toggle diff (38 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 21aa3476c0..71d65d64a5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9420,6 +9420,31 @@ (define-public r-apalyzer
expression analysis using RNA-seq data.")
(license license:lgpl3)))
+(define-public r-apcomplex
+ (package
+ (name "r-apcomplex")
+ (version "2.64.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "apComplex" version))
+ (sha256
+ (base32 "0ycchrdhx7zh62f0p0gxm7g58m2w3c2lfkaasrwydspd3jx0rsna"))))
+ (properties `((upstream-name . "apComplex")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-graph
+ r-org-sc-sgd-db
+ r-rbgl
+ r-rgraphviz))
+ (home-page "https://bioconductor.org/packages/apComplex")
+ (synopsis "Estimate protein complex membership using AP-MS protein data")
+ (description
+ "This package provides functions to estimate a bipartite graph of protein
+complex membership using @acronym{AP-MS, affinity purification–mass spectrometry}
+data.")
+ (license license:lgpl2.0+)))
+
(define-public r-apeglm
(package
(name "r-apeglm")
--
2.39.2
M
M
M?d?lin Ionel Patra?cu wrote on 25 Mar 2023 00:18
[PATCH 08/14] gnu: Add r-parody.
20230324231900.28367-8-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-parody): New variable.
---
gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++
1 file changed, 21 insertions(+)

Toggle diff (34 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 39367dd927..9f43c42bee 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -18999,6 +18999,27 @@ (define-public r-spp
other functional sequencing data.")
(license license:gpl2)))
+(define-public r-parody
+ (package
+ (name "r-parody")
+ (version "1.56.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "parody" version))
+ (sha256
+ (base32 "12i5g4ai7a0p81kvqvz1qw099cy3g71n69pij8w760r3jn0c9ilw"))))
+ (properties `((upstream-name . "parody")))
+ (build-system r-build-system)
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/parody")
+ (synopsis "Parametric and resistant outlier dytection")
+ (description
+ "The parody package provides routines for univariate and multivariate outlier
+detection with a focus on parametric methods, but support for some methods based
+on resistant statistics.")
+ (license license:artistic2.0)))
+
(define-public r-pathview
(package
(name "r-pathview")
--
2.39.2
M
M
M?d?lin Ionel Patra?cu wrote on 25 Mar 2023 00:18
[PATCH 12/14] gnu: Add r-beaddatapackr.
20230324231900.28367-12-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-beaddatapackr): New variable.
---
gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++
1 file changed, 20 insertions(+)

Toggle diff (33 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7a904d3d08..e7ab9c983c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -17963,6 +17963,26 @@ (define-public r-beadarraysnp
performs copy number calculations and reports.")
(license license:gpl2)))
+(define-public r-beaddatapackr
+ (package
+ (name "r-beaddatapackr")
+ (version "1.50.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BeadDataPackR" version))
+ (sha256
+ (base32 "0309cvc9aq4nb06zysb7jvzd844pvw6jbjiqwhar6fg01cx255j0"))))
+ (properties `((upstream-name . "BeadDataPackR")))
+ (build-system r-build-system)
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/BeadDataPackR")
+ (synopsis "Compression of Illumina BeadArray data")
+ (description
+ "This package provides functionality for the compression and decompression
+of raw bead-level data from the Illumina BeadArray platform.")
+ (license license:gpl2)))
+
;; This package includes files that have been taken from kentutils. Some
;; parts of kentutils are not released under a free license, but this package
;; only uses files that are also found in the free parts of kentutils.
--
2.39.2
M
M
M?d?lin Ionel Patra?cu wrote on 25 Mar 2023 00:18
[PATCH 10/14] gnu: Add r-arrayquality.
20230324231900.28367-10-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-arrayquality): New variable.
---
gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)

Toggle diff (38 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 62cd786842..7a904d3d08 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3251,6 +3251,31 @@ (define-public r-arraymvout
error rate.")
(license license:artistic2.0)))
+(define-public r-arrayquality
+ (package
+ (name "r-arrayquality")
+ (version "1.76.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "arrayQuality" version))
+ (sha256
+ (base32 "0b5q71bpl9ln26622jvchd4f9i4kwayqkm9b75yj0a69imbfcn4s"))))
+ (properties `((upstream-name . "arrayQuality")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-gridbase
+ r-hexbin
+ r-limma
+ r-marray
+ r-rcolorbrewer))
+ (home-page "http://arrays.ucsf.edu/")
+ (synopsis "Assessing array quality on spotted arrays")
+ (description
+ "This package provides functions for performing print-run and array level
+quality assessment.")
+ (license license:lgpl2.0+)))
+
(define-public r-asafe
(package
(name "r-asafe")
--
2.39.2
M
M
M?d?lin Ionel Patra?cu wrote on 25 Mar 2023 00:18
[PATCH 09/14] gnu: Add r-arraymvout.
20230324231900.28367-9-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-arraymvout): New variable.
---
gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++++
1 file changed, 36 insertions(+)

Toggle diff (49 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9f43c42bee..62cd786842 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3215,6 +3215,42 @@ (define-public r-arrayexpress
structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.")
(license license:artistic2.0)))
+(define-public r-arraymvout
+ (package
+ (name "r-arraymvout")
+ (version "1.56.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "arrayMvout" version))
+ (sha256
+ (base32 "0g66s64n4qlvhkanp33bbvpi93rsdx5xq0mjr96d0195qbf6k156"))))
+ (properties `((upstream-name . "arrayMvout")))
+ (build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'install 'change-home-dir
+ (lambda _
+ ;; Change from /homeless-shelter to /tmp for write permission.
+ (setenv "HOME" "/tmp"))))))
+ (propagated-inputs
+ (list r-affy
+ r-affycontam
+ r-biobase
+ r-lumi
+ r-mdqc
+ r-parody))
+ (home-page "https://bioconductor.org/packages/arrayMvout")
+ (synopsis "Multivariate outlier detection for expression array QA")
+ (description
+ "This package supports the application of diverse quality metrics to AffyBatch
+instances, summarizing these metrics via PCA, and then performing parametric
+outlier detection on the PCs to identify aberrant arrays with a fixed Type I
+error rate.")
+ (license license:artistic2.0)))
+
(define-public r-asafe
(package
(name "r-asafe")
--
2.39.2
M
M
M?d?lin Ionel Patra?cu wrote on 25 Mar 2023 00:18
[PATCH 13/14] gnu: Add r-beadarray.
20230324231900.28367-13-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-beadarray): New variable.
---
gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)

Toggle diff (47 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e7ab9c983c..6c114efd21 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -17943,6 +17943,40 @@ (define-public r-beachmat
matrices.")
(license license:gpl3)))
+(define-public r-beadarray
+ (package
+ (name "r-beadarray")
+ (version "2.48.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "beadarray" version))
+ (sha256
+ (base32 "0fr24gj6h2rr1r4l3n8myjaihjqi5yinwdsxqa5ih8m3v72dlrby"))))
+ (properties `((upstream-name . "beadarray")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-annotationdbi
+ r-beaddatapackr
+ r-biobase
+ r-biocgenerics
+ r-genomicranges
+ r-ggplot2
+ r-hexbin
+ r-illuminaio
+ r-iranges
+ r-limma
+ r-reshape2))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/beadarray")
+ (synopsis
+ "Quality assessment and low-level analysis for Illumina BeadArray data")
+ (description
+ "The package is able to read bead-level data (raw TIFFs and text files)
+output by BeadScan as well as bead-summary data from BeadStudio. Methods for
+quality assessment and low-level analysis are provided.")
+ (license license:expat)))
+
(define-public r-beadarraysnp
(package
(name "r-beadarraysnp")
--
2.39.2
M
M
M?d?lin Ionel Patra?cu wrote on 25 Mar 2023 00:19
[PATCH 14/14] gnu: Add r-arrayqualitymetrics.
20230324231900.28367-14-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-arrayqualitymetrics): New variable.
---
gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)

Toggle diff (51 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6c114efd21..8792c94d29 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3190,6 +3190,44 @@ (define-public r-antiprofiles
tumor samples from healthy controls.")
(license license:artistic2.0)))
+(define-public r-arrayqualitymetrics
+ (package
+ (name "r-arrayqualitymetrics")
+ (version "3.54.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "arrayQualityMetrics" version))
+ (sha256
+ (base32 "0jz9b3f8x1aal4sskq1a09jpavhm8alggwbj3ka42fb89xymrz33"))))
+ (properties `((upstream-name . "arrayQualityMetrics")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-affy
+ r-affyplm
+ r-beadarray
+ r-biobase
+ r-genefilter
+ r-gridsvg
+ r-hmisc
+ r-hwriter
+ r-lattice
+ r-latticeextra
+ r-limma
+ r-rcolorbrewer
+ r-setrng
+ r-svglite
+ r-vsn
+ r-xml))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/arrayQualityMetrics")
+ (synopsis "Quality metrics report for microarray data sets")
+ (description
+ "This package generates microarray quality metrics reports for data in
+Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch).
+One and two color array platforms are supported.")
+ (license license:lgpl2.0+)))
+
(define-public r-arrayexpress
(package
(name "r-arrayexpress")
--
2.39.2
M
M
M?d?lin Ionel Patra?cu wrote on 25 Mar 2023 00:18
[PATCH 11/14] gnu: Add r-setrng.
20230324231900.28367-11-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/cran.scm (r-setrng): New variable.
---
gnu/packages/cran.scm | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)

Toggle diff (35 lines)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 325fec402b..bfcafea355 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -20170,6 +20170,28 @@ (define-public r-bedr
additional utilities for genomic regions processing.")
(license license:gpl2)))
+(define-public r-setrng
+ (package
+ (name "r-setrng")
+ (version "2022.4-1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "setRNG" version))
+ (sha256
+ (base32 "09089vr5x8snwxh38kdhgpjl3jl7zrk056f6f9a2jg5lsrmnxh31"))))
+ (properties `((upstream-name . "setRNG")))
+ (build-system r-build-system)
+ (home-page "http://distr.r-forge.r-project.org/")
+ (synopsis "Set (normal) random number generator and seed")
+ (description
+ "This package provides utilities to help set and record the setting of the
+seed and the uniform and normal generators used when a random experiment is run.
+The utilities can be used in other functions that do random experiments to simplify
+recording and/or setting all the necessary information for reproducibility. See
+the vignette and reference manual for examples.")
+ (license license:gpl2)))
+
(define-public r-sets
(package
(name "r-sets")
--
2.39.2
B
B
Bruno Victal wrote on 31 Mar 2023 01:00
control-msg
(name . control)(address . control@debbugs.gnu.org)
74912071-f536-c8bc-4711-db295b4da0e6@makinata.eu
# done with 5c131aff691fa1cb0fafe71b5f2795902ae056a7
close 55819

# control fail?
close 45449

# no longer relevant
close 33078

# tags
tags 62551 patch
tags 62503 patch
tags 62461 patch
tags 62443 patch
tags 62428 patch
tags 61226 patch
tags 59893 patch
tags 59852 patch
tags 49451 patch
tags 49207 patch
tags 44258 patch


quit
R
R
Ricardo Wurmus wrote on 4 Oct 2023 11:06
gnu: Add r-anota2seq …
(address . 62428-done@debbugs.gnu.org)
878r8irc1l.fsf@elephly.net
I’ve rebased this, updated all packages, fixed indentation, replaced
gexp syntax with simple quote, and removed duplicates.

Thanks for the patches! Closing.

--
Ricardo
Closed
?