MadalinIonel.Patrascu@mdc-berlin.de wrote 3 years ago
(name . guix-patches@gnu.org)(address . guix-patches@gnu.org)
7c12946df28042ceb9b9a3b266551f55@mdc-berlin.de
gnu: Add r-scmap add r-googlevis.
- 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-scmap.
(address . 55679@debbugs.gnu.org)
20220527164013.4195-2-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-scmap): New variable.
---
gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++
1 file changed, 41 insertions(+)
Toggle diff (54 lines)
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
Mădălin Ionel Patrașcu wrote 3 years ago
[PATCH 1/2] gnu: Add r-googlevis.
(address . 55679@debbugs.gnu.org)
20220527164013.4195-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/cran.scm (r-googlevis): New variable.
---
gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
Toggle diff (42 lines)
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
Ricardo Wurmus wrote 3 years ago
(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 55679-done@debbugs.gnu.org)
87o7zhb7kx.fsf@elephly.net
Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:
Toggle quote (2 lines)
> * gnu/packages/cran.scm (r-googlevis): New variable.
I applied this and the patch for r-scmap after minor formatting
changes. Thanks!
--
Ricardo
Closed
?