GNU bug report logs - #56819
gnu: Add r-phyclust and r-infercnv. (New variables)

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: "MadalinIonel.Patrascu <at> mdc-berlin.de"
 <MadalinIonel.Patrascu <at> mdc-berlin.de>
To: "guix-patches <at> gnu.org" <guix-patches <at> gnu.org>
Subject: gnu: Add r-phyclust and r-infercnv. (New variables)
Date: Thu, 28 Jul 2022 21:35:36 +0000

[Message part 1 (text/plain, inline)]

[Message part 2 (text/html, inline)]

Message #8 received at 56819 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <56819 <at> debbugs.gnu.org>
Subject: [PATCH 2/2] gnu: Add r-infercnv.
Date: Thu, 28 Jul 2022 23:38:59 +0200

* gnu/packages/bioconductor.scm (r-infercnv): New variable.
---
 gnu/packages/bioconductor.scm | 60 +++++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)

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

Message #11 received at 56819 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <56819 <at> debbugs.gnu.org>
Subject: [PATCH 1/2] gnu: Add r-phyclust.
Date: Thu, 28 Jul 2022 23:38:58 +0200

* gnu/packages/cran.scm (r-phyclust): New variable.
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

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

Message #14 received at 56819 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 56819 <at> debbugs.gnu.org
Subject: Re: [bug#56819] [PATCH 2/2] gnu: Add r-infercnv.
Date: Mon, 01 Aug 2022 16:20:12 +0200

Mădălin Ionel Patrașcu <madalinionel.patrascu <at> 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.

-- 
Ricardo

Message #19 received at 56819-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 56819-done <at> debbugs.gnu.org
Subject: Re: [bug#56819] [PATCH 2/2] gnu: Add r-infercnv.
Date: Tue, 02 Aug 2022 10:23:02 +0200

Ricardo Wurmus <rekado <at> elephly.net> writes:

> Mădălin Ionel Patrașcu <madalinionel.patrascu <at> 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

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