Mădălin Ionel Patrașcu wrote 4 years ago
(address . guix-patches@gnu.org)
955092cf-b234-26a5-88df-7e7d9911a729@mdc-berlin.de
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- Mădălin Ionel Patrașcu
- Ricardo Wurmus
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- Mădălin Ionel Patrașcu
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Mădălin Ionel Patrașcu wrote 4 years ago
[PATCH 1/2] gnu: Add r-kegggraph.
(address . 45282@debbugs.gnu.org)(address . rekado@elephly.net)(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)
20201216220342.3133-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-kegggraph): New variable.
---
gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++
1 file changed, 26 insertions(+)
Toggle diff (36 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b4a1af4306..3026d1a496 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9247,3 +9247,29 @@ graph with the mapped data. In addition, @code{r-pathview} also seamlessly
integrates with pathway and gene set (enrichment) analysis tools for
large-scale and fully automated analysis.")
(license license:gpl3+)))
+
+(define-public r-kegggraph
+ (package
+ (name "r-kegggraph")
+ (version "1.50.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "KEGGgraph" version))
+ (sha256
+ (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v"))))
+ (properties `((upstream-name . "KEGGgraph")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-graph" ,r-graph)
+ ("r-rcurl" ,r-rcurl)
+ ("r-xml" ,r-xml)))
+ (home-page "http://www.nextbiomotif.com") ;;no https
+ (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
+ (description
+ "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
+object as well as a collection of tools to analyze, dissect and visualize these
+graphs. It parses the regularly updated kgml (Kegg xml) files into graph models
+maintaining all essential pathway attributes. The package offers
+functionalities including parsing, graph operation, visualization and etc.")
+ (license license:gpl2+)))
--
2.29.2
Mădălin Ionel Patrașcu wrote 4 years ago
[PATCH 2/2] gnu: Add r-pathview.
(address . 45282@debbugs.gnu.org)(address . rekado@elephly.net)(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)
20201216221533.3539-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-pathview): New variable.
---
gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)
Toggle diff (44 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 36274d0b39..b4a1af4306 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9213,3 +9213,37 @@ on KEGG pathways and GO terms for major research species, including human,
mouse, rat and budding yeast. Mapping data between common gene IDs for budding
yeast are also included.")
(license license:gpl2+)))
+
+(define-public r-pathview
+ (package
+ (name "r-pathview")
+ (version "1.30.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "pathview" version))
+ (sha256
+ (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4"))))
+ (properties `((upstream-name . "pathview")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-graph" ,r-graph)
+ ("r-kegggraph" ,r-kegggraph)
+ ("r-keggrest" ,r-keggrest)
+ ("r-org-hs-eg-db" ,r-org-hs-eg-db)
+ ("r-png" ,r-png)
+ ("r-rgraphviz" ,r-rgraphviz)
+ ("r-xml" ,r-xml)))
+ (home-page "https://pathview.uncc.edu/")
+ (synopsis "Tool set for pathway based data integration and visualization")
+ (description
+ "@code{r-pathview} is a tool set for pathway based data integration and
+visualization. It maps and renders a wide variety of biological data on
+relevant pathway graphs. All users need is to supply their data and specify
+the target pathway. This package automatically downloads the pathway graph
+data, parses the data file, maps user data to the pathway, and render pathway
+graph with the mapped data. In addition, @code{r-pathview} also seamlessly
+integrates with pathway and gene set (enrichment) analysis tools for
+large-scale and fully automated analysis.")
+ (license license:gpl3+)))
--
2.29.2
Ricardo Wurmus wrote 4 years ago
Re: [PATCH 1/2] gnu: Add r-kegggraph.
(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 45282-done@debbugs.gnu.org)
87lfdwoegw.fsf@elephly.net
I applied these with a few changes (moved the packages around and
reordered the commits).
Thanks!
--
Ricardo
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