MadalinIonel.Patrascu@mdc-berlin.de wrote 3 years ago
(name . guix-patches@gnu.org)(address . guix-patches@gnu.org)
3f5cff2631864372b7a0b1233e11ce86@mdc-berlin.de
gnu: Add r-phyclust and r-infercnv. (New variables)
- Done
Details
- 3 participants
- MadalinIonel.Patrascu@mdc-berlin.de
- Mădălin Ionel Patrașcu
- Ricardo Wurmus
- Owner
- unassigned
- Submitted by
- MadalinIonel.Patrascu@mdc-berlin.de
- Severity
- normal
Mădălin Ionel Patrașcu wrote 3 years ago
[PATCH 2/2] gnu: Add r-infercnv.
(address . 56819@debbugs.gnu.org)
20220728213859.21641-2-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-infercnv): New variable.
---
gnu/packages/bioconductor.scm | 60 +++++++++++++++++++++++++++++++++++
1 file changed, 60 insertions(+)
Toggle diff (80 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 31484799b2..e9bfbed9b5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -49,6 +49,7 @@ (define-module (gnu packages bioconductor)
#:use-module (gnu packages image)
#:use-module (gnu packages maths)
#:use-module (gnu packages netpbm)
+ #:use-module (gnu packages python)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages statistics)
@@ -2647,6 +2648,65 @@ (define-public r-ideoviz
arbitrary genomic intervals along chromosomal ideogram.")
(license license:gpl2)))
+(define-public r-infercnv
+ (package
+ (name "r-infercnv")
+ (version "1.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "infercnv" version))
+ (sha256
+ (base32
+ "01f021fdxm058733rky46dlvqg7dmf5mn5x9lnq0fspp5665w3bl"))))
+ (properties `((upstream-name . "infercnv")))
+ (build-system r-build-system)
+ (inputs (list python))
+ (propagated-inputs
+ (list r-ape
+ r-argparse
+ r-biocgenerics
+ r-catools
+ r-coda
+ r-coin
+ r-digest
+ r-doparallel
+ r-dplyr
+ r-edger
+ r-fastcluster
+ r-fitdistrplus
+ r-foreach
+ r-futile-logger
+ r-future
+ r-ggplot2
+ r-gplots
+ r-gridextra
+ r-hiddenmarkov
+ r-leiden
+ r-matrix
+ r-paralleldist
+ r-phyclust
+ r-rann
+ r-rcolorbrewer
+ r-reshape
+ r-rjags
+ r-singlecellexperiment
+ r-summarizedexperiment
+ r-tidyr))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/broadinstitute/inferCNV/wiki")
+ (synopsis "Infer copy number variation from single-cell RNA-Seq data")
+ (description
+ "@code{InferCNV} is used to explore tumor single cell RNA-Seq data to identify
+evidence for somatic large-scale chromosomal copy number alterations, such as gains
+or deletions of entire chromosomes or large segments of chromosomes. This is done
+by exploring expression intensity of genes across positions of a tumor genome in
+comparison to a set of reference \"normal\" cells. A heatmap is generated
+illustrating the relative expression intensities across each chromosome, and it
+often becomes readily apparent as to which regions of the tumor genome are
+over-abundant or less-abundant as compared to that of normal cells.")
+ (license license:bsd-3)))
+
(define-public r-iranges
(package
(name "r-iranges")
--
2.37.1
Mădălin Ionel Patrașcu wrote 3 years ago
[PATCH 1/2] gnu: Add r-phyclust.
(address . 56819@debbugs.gnu.org)
20220728213859.21641-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/cran.scm (r-phyclust): New variable.
---
gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
Toggle diff (40 lines)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 731facb4e5..e63cb28e19 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11699,6 +11699,31 @@ (define-public r-nleqslv
singular or ill-conditioned Jacobian.")
(license license:gpl2+)))
+(define-public r-phyclust
+ (package
+ (name "r-phyclust")
+ (version "0.1-30")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "phyclust" version))
+ (sha256
+ (base32
+ "0fy9q95vmlm9idpax7alhpfwn30gflnc9md72g91jypyxkx5nr7p"))))
+ (properties `((upstream-name . "phyclust")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-ape))
+ (home-page "https://snoweye.github.io/phyclust/")
+ (synopsis "Studying phyloclustering and exploring DNA sequence data")
+ (description
+ "@dfn{Phylogenetic clustering} (phyloclustering) is an evolutionary continuous
+time Markov Chain model-based approach to identify population structure from
+molecular data without assuming linkage equilibrium. The package @code{phyclust}
+provides a convenient implementation of phyloclustering for DNA and SNP data,
+capable of clustering individuals into subpopulations and identifying molecular
+sequences representative of those subpopulations. It is designed in @code{C} for
+performance and interfaced with @code{R} for visualization.")
+ (license license:gpl2+)))
+
(define-public r-physicalactivity
(package
(name "r-physicalactivity")
base-commit: bdb2e262fcbea76de807cd829c2d2270661546a5
--
2.37.1
Ricardo Wurmus wrote 3 years ago
Re: [bug#56819] [PATCH 2/2] gnu: Add r-infercnv.
(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 56819@debbugs.gnu.org)
87k07sniyl.fsf@elephly.net
Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:
Toggle quote (1 lines)
> * gnu/packages/bioconductor.scm (r-infercnv): New variable.
[…]
Toggle quote (2 lines)
> + r-phyclust
This variable is not defined anywhere, or maybe I just can’t find it.
--
Ricardo
Ricardo Wurmus wrote 3 years ago
(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 56819-done@debbugs.gnu.org)
87pmhjm4sy.fsf@elephly.net
Ricardo Wurmus <rekado@elephly.net> writes:
Toggle quote (8 lines)
> Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:
>
>> * gnu/packages/bioconductor.scm (r-infercnv): New variable.
> […]
>> + r-phyclust
>
> This variable is not defined anywhere, or maybe I just can’t find it.
The problem was that I only received the second email; the first one
wasn’t cc’d to me. I then saw that the first patch is right there on
issues.guix.gnu.org, so I applied them both.
Sorry for the confusion!
--
Ricardo
Closed
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