[bug#54620] [PATCH 1/3] Add r-rafalib

[bug#54620] [PATCH 1/3] Add r-rafalib

[Hong.Li]

[-- Attachment #1.1: Type: text/plain, Size: 2 bytes --]



[-- Attachment #1.2: Type: text/html, Size: 368 bytes --]

[-- Attachment #2: 0001-Add-r-rafalib.patch --]
[-- Type: application/octet-stream, Size: 1345 bytes --]

From 5d7cc7fa04bfe2b63dcaeed90359b81fd7ed0679 Mon Sep 17 00:00:00 2001
From: "Li, Hong" <hong.li@mdc-berlin.de>
Date: Mon, 28 Mar 2022 11:39:39 +0200
Subject: [PATCH 1/3] Add r-rafalib

---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 23645faa8a..e595de6c2d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7464,6 +7464,26 @@ files.")
 environment within Shiny.")
     (license license:expat)))
 
+(define-public r-rafalib
+  (package
+    (name "r-rafalib")
+    (version "1.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "rafalib" version))
+        (sha256
+          (base32 "1dmxjl66bfdgrybhwyaa8d4i460liqcdw8b29a6w7shgksh29m0k"))))
+    (properties `((upstream-name . "rafalib")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-rcolorbrewer))
+    (home-page "https://cran.r-project.org/package=rafalib")
+    (synopsis "Convenience Functions for Routine Data Exploration")
+    (description
+      "This package provides a series of shortcuts for routine tasks originally
+developed by Rafael A.  Irizarry to facilitate data exploration.")
+    (license license:artistic2.0)))
+
 (define-public r-randomizr
   (package
     (name "r-randomizr")
-- 
2.26.1

[bug#54620] [PATCH 2/3] Add r-stager

[Hong.Li]

[-- Attachment #1.1: Type: text/plain, Size: 2 bytes --]



[-- Attachment #1.2: Type: text/html, Size: 368 bytes --]

[-- Attachment #2: 0002-Add-r-stager.patch --]
[-- Type: application/octet-stream, Size: 1596 bytes --]

From 5c0016a8e9b905e6eeae1d682b9db16379030e94 Mon Sep 17 00:00:00 2001
From: "Li, Hong" <hong.li@mdc-berlin.de>
Date: Mon, 28 Mar 2022 11:41:51 +0200
Subject: [PATCH 2/3] Add r-stager

---
 gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 55d397e5cf..c22199528e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4739,6 +4739,29 @@ events and allows for the incorporation of prior knowledge through supervised
 graph construction.")
    (license license:artistic2.0)))
 
+(define-public r-stager
+  (package
+    (name "r-stager")
+    (version "1.16.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (bioconductor-uri "stageR" version))
+        (sha256
+          (base32 "0vpx0v04hgkhzi0bm7ipnb9xr37n5wvnnr45lljgni8pwabfkf6y"))))
+    (properties `((upstream-name . "stageR")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/stageR")
+    (synopsis
+      "stageR: stage-wise analysis of high throughput gene expression data")
+    (description
+      "The stageR package allows automated stage-wise analysis of high-throughput gene
+expression data.  The method is published in Genome Biology at
+https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0")
+    (license license:#f)))
+
 (define-public r-stringdb
   (package
     (name "r-stringdb")
-- 
2.26.1

[bug#54620] [PATCH 3/3] Add r-rnaseqdtu

[Hong.Li]

[-- Attachment #1.1: Type: text/plain, Size: 2 bytes --]



[-- Attachment #1.2: Type: text/html, Size: 368 bytes --]

[-- Attachment #2: 0003-Add-r-rnaseqdtu.patch --]
[-- Type: application/octet-stream, Size: 2289 bytes --]

From fdd03ffe8b0db96f4ba662c0367a012267659a30 Mon Sep 17 00:00:00 2001
From: "Li, Hong" <hong.li@mdc-berlin.de>
Date: Mon, 28 Mar 2022 11:44:35 +0200
Subject: [PATCH 3/3] Add r-rnaseqdtu

---
 gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ada5965e5f..c79d4ad82d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9009,6 +9009,43 @@ for analyzing gene-level association tests in meta-analyses for binary
 trait.")
     (license license:gpl3)))
 
+(define-public r-rnaseqdtu
+  (let ((commit "5bee1e769d2e1dc6a3f1cecb78078050eeb5b9ac") (revision "1"))
+    (package
+      (name "r-rnaseqdtu")
+      (version (git-version "2.0" revision commit))
+      (source
+        (origin
+          (method git-fetch)
+          (uri (git-reference
+                 (url "https://github.com/mikelove/rnaseqDTU/")
+                 (commit commit)))
+          (file-name (git-file-name name version))
+          (sha256
+            (base32 "0jfi1ydsk8m5nadwnih48v87nnxdc7s3f0pny4axmnj40dd42as0"))))
+      (properties `((upstream-name . "rnaseqDTU")))
+      (build-system r-build-system)
+      (propagated-inputs
+        (list r-deseq2
+              r-devtools
+              r-dexseq
+              r-drimseq
+              r-edger
+              r-rafalib
+              r-stager))
+      (native-inputs (list r-knitr))
+      (home-page "https://github.com/mikelove/rnaseqDTU/")
+      (synopsis
+        "RNA-seq workflow for differential transcript usage following Salmon quantification")
+      (description
+        "RNA-seq workflow for differential transcript usage (DTU) following Salmon
+quantification.  This workflow uses Bioconductor packages tximport, DRIMSeq, and
+DEXSeq to perform a DTU analysis on simulated data.  It also shows how to use
+stageR to perform two-stage testing of DTU, a statistical framework to screen at
+the gene level and then confirm which transcripts within the significant genes
+show evidence of DTU.")
+      (license license:artistic2.0))))
+
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.26.1

bug#54620: [PATCH 3/3] Add r-rnaseqdtu

[Ricardo Wurmus]

Thanks for the patches!  I modified them to fix licenses, descriptions,
synopses, indentation, etc, and just pushed them to the “master” branch.

-- 
Ricardo