[bug#55679] gnu: Add r-scmap add r-googlevis.

[bug#55679] gnu: Add r-scmap add r-googlevis.

[MadalinIonel.Patrascu]

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[bug#55679] [PATCH 1/2] gnu: Add r-googlevis.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-googlevis): New variable.
---
 gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 0fdcfb3cb9..ae90e5f162 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -402,6 +402,33 @@ (define-public r-googledrive
     (description "This package lets you manage Google Drive files from R.")
     (license license:expat)))
 
+(define-public r-googlevis
+  (package
+    (name "r-googlevis")
+    (version "0.7.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "googleVis" version))
+        (sha256
+          (base32 "1s82xcs6zrlmnhay764bspzwvabfyi35nq6fwdrrk3v79q13c5jz"))))
+    (properties `((upstream-name . "googleVis")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-jsonlite))
+    (native-inputs (list r-knitr))
+    (home-page "https://mages.github.io/googleVis/")
+    (synopsis "R interface to Google Charts")
+    (description
+      "The @code{googleVis} package provides an interface between R and the
+Google Charts API.  Google Charts offer interactive charts which can be embedded
+into web pages.  The functions of the @code{googleVis} package allow the user to
+visualise data stored in @code{R} data frames with Google Charts without
+uploading the data to Google.  The output of a @code{googleVis} function is
+@code{HTML} code that contains the data and references to JavaScript functions
+hosted by Google.  @code{googleVis} makes use of the internal @code{R}
+@code{HTTP server} to display the output locally.")
+    (license license:gpl2+)))
+
 (define-public r-guix-install
   (package
     (name "r-guix-install")

base-commit: 0e953f3332cc862b08ecb2342bdac9976dd6d08c
-- 
2.36.0

[bug#55679] [PATCH 2/2] gnu: Add r-scmap.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-scmap): New variable.
---
 gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4baa80dcb1..9c6526331e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5049,6 +5049,47 @@ (define-public r-scdblfinder
 comprehensive scDblFinder method.")
     (license license:gpl3)))
 
+(define-public r-scmap
+  (package
+    (name "r-scmap")
+    (version "1.18.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (bioconductor-uri "scmap" version))
+        (sha256
+          (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l"))))
+    (properties `((upstream-name . "scmap")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biobase
+           r-biocgenerics
+           r-dplyr
+           r-e1071
+           r-ggplot2
+           r-googlevis
+           r-matrixstats
+           r-proxy
+           r-randomforest
+           r-rcpp
+           r-rcpparmadillo
+           r-reshape2
+           r-s4vectors
+           r-singlecellexperiment
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/hemberg-lab/scmap")
+    (synopsis "Tool for unsupervised projection of single cell RNA-seq data")
+    (description
+     "@dfn{Single-cell RNA-seq} (scRNA-seq) is widely used to investigate the
+composition of complex tissues since the technology allows researchers to define
+cell-types using unsupervised clustering of the transcriptome.  However, due to
+differences in experimental methods and computational analyses, it is often
+challenging to directly compare the cells identified in two different experiments.
+@code{scmap} is a method for projecting cells from a scRNA-seq experiment onto
+the cell-types or individual cells identified in a different experiment.")
+    (license license:gpl3)))
+
 (define-public r-seqlogo
   (package
     (name "r-seqlogo")
-- 
2.36.0

bug#55679: [PATCH 1/2] gnu: Add r-googlevis.

[Ricardo Wurmus]

Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:

> * gnu/packages/cran.scm (r-googlevis): New variable.

I applied this and the patch for r-scmap after minor formatting
changes.  Thanks!

-- 
Ricardo