[bug#61250] [PATCH 1/3] gnu: Add r-viper.

[bug#61250] [PATCH 1/3] gnu: Add r-viper.

[Navid Afkhami]

* gnu/packages/bioconductor.scm (r-viper): New variable.
---
 gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 711b988e7f..aeef6f4106 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8307,6 +8307,27 @@ (define-public r-variantannotation
 coding changes and predict coding outcomes.")
     (license license:artistic2.0)))
 
+(define-public r-viper
+  (package
+    (name "r-viper")
+    (version "1.32.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "viper" version))
+              (sha256
+               (base32
+                "11i2q9nakh534nx2l736id7k1yqhk7jpg32sbfl4vrnh398q86h6"))))
+    (properties `((upstream-name . "viper")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biobase r-e1071 r-kernsmooth r-mixtools))
+    (home-page "https://bioconductor.org/packages/viper")
+    (synopsis
+     "Virtual inference of protein-activity by enriched regulon analysis")
+    (description
+     "Inference of protein activity from gene expression data.
+Including the VIPER and msVIPER algorithms")
+    (license license:gpl2+)))
+
 (define-public r-vsn
   (package
     (name "r-vsn")
-- 
2.34.1

[bug#61251] [PATCH 2/3] gnu: Add r-bcellviper.

[Navid Afkhami]

* gnu/packages/bioconductor.scm (r-bcellviper): New variable.
---
 gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index aeef6f4106..521d6c00be 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1248,6 +1248,29 @@ (define-public r-arrmdata
 from Illumina 450k methylation arrays.")
     (license license:artistic2.0)))
 
+(define-public r-bcellviper
+  (package
+    (name "r-bcellviper")
+    (version "1.34.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "bcellViper" version
+                                     'experiment))
+              (sha256
+               (base32
+                "1fpgh70x2r68v0ximgcdphnyzq2hgiwbamyhbac3yka8flhrd1fm"))))
+    (properties `((upstream-name . "bcellViper")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biobase))
+    (home-page "https://bioconductor.org/packages/bcellViper")
+    (synopsis
+     "Transcriptional interactome and normal human B-cell expression data")
+    (description
+     "This is a tool for human B-cell context-specific transcriptional regulatory network.
+In addition, this package provides a human normal B-cells dataset for
+the examples in package viper.")
+    (license license:gpl2+)))
+
 (define-public r-bladderbatch
   (package
     (name "r-bladderbatch")
-- 
2.34.1

[bug#61252] [PATCH 3/3] gnu: Add r-dorothea.

[Navid Afkhami]

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 521d6c00be..0786160b5e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -466,6 +466,31 @@ (define-public r-bsgenome-mmusculus-ucsc-mm10
 in Biostrings objects.")
     (license license:artistic2.0)))
 
+(define-public r-dorothea
+  (package
+    (name "r-dorothea")
+    (version "1.10.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "dorothea" version
+                                     'experiment))
+              (sha256
+               (base32
+                "05vkb5mash2m8p6njk842sy5pz7vblrm8n9bphqbslm86kld5n92"))))
+    (properties `((upstream-name . "dorothea")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-bcellviper r-dplyr r-magrittr r-viper))
+    (native-inputs (list r-knitr))
+    (home-page "https://saezlab.github.io/dorothea/")
+    (synopsis "Collection of human and mouse TF regulons")
+    (description
+     "DoRothEA is a gene regulatory network containing signed transcription factor.
+DoRothEA regulons, the collection of a TF andits transcriptional targets,
+were curated and collected from different types ofevidence for both human
+and mouse.  A confidence level was assigned to each TF-target interaction
+based on the number of supporting evidence.")
+    (license license:gpl3)))
+
 (define-public r-genomeinfodbdata
   (package
     (name "r-genomeinfodbdata")
-- 
2.34.1

bug#61250: [PATCH 1/3] gnu: Add r-viper.

[Ricardo Wurmus]

Unfortunately, we cannot add this to Guix.   The license says:

  c. You agree that You will only use the Program and Documentation for
     non-commercial internal academic or educational research purposes
     only. You will not (i) reproduce or copy the Program (ii) use, or
     cause or permit the use of, the Program in whole or in part for any
     purpose other than as permitted under this License; (iii)
     distribute, sell, lease, license or otherwise make the Program
     available to a third party outside Your organization; or (iv)
     reverse engineer, decompile, or disassemble the Program.

I have instead added the package to guix-science-nonfree.

-- 
Ricardo

bug#61251: [PATCH 2/3] gnu: Add r-bcellviper.

[Ricardo Wurmus]

Applied, thanks!

-- 
Ricardo

bug#61252: [PATCH 3/3] gnu: Add r-dorothea.

[Ricardo Wurmus]

Thanks for the patch!

Since this depends on r-viper, which is nonfree I cannot add this
package to Guix.  I have instead pushed it to the channel
“guix-science-nonfree”.

-- 
Ricardo