From: hong li <hongli520@gmail.com>
To: 47314@debbugs.gnu.org
Subject: [bug#47314] [Patch] two r packages (chromstardata and signac)
Date: Mon, 22 Mar 2021 11:12:07 +0100 [thread overview]
Message-ID: <CACnRHThdKzAjgbhse3nZTOXM6Mn4LuSYSTVoLe-Bio_GqsV=ww@mail.gmail.com> (raw)
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Dear Guixer,
I have sent a email last week to add two r packages into guix, here is the
patch.
please help to add them to the guix store.
Thanks.
best regards,
Hong Li
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From 1c51dff18a6a9508bd11dd95f07be4dc4fb9c542 Mon Sep 17 00:00:00 2001
From: hli <hli@mdc-berlin.de>
Date: Mon, 22 Mar 2021 11:00:47 +0100
Subject: [PATCH] adding r-chromstardata and r-signac packages
---
gnu/packages/statistics.scm | 127 ++++++++++++++++++++++++++++++++++++
1 file changed, 127 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 27f3bfa8ef..0cf026fcfb 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1035,6 +1035,65 @@ designed by Cynthia Brewer as described at http://colorbrewer2.org")
solution for sending email, including attachments, from within R.")
(license license:gpl2+)))
+(define-public r-signac
+ (let ((commit
+ "e0512d348adeda4a3f23a2e8f56d1fe09840e03c")
+ (revision "1"))
+ (package
+ (name "r-signac")
+ (version (git-version "1.1.1" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/timoast/signac/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1yihhrv7zs87ax61la1nb4y12lg3knraw4b20k5digbcwm8488lb"))))
+ (properties `((upstream-name . "Signac")))
+ (build-system r-build-system)
+ (inputs `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-annotationfilter" ,r-annotationfilter)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-biovizbase" ,r-biovizbase)
+ ("r-data-table" ,r-data-table)
+ ("r-dplyr" ,r-dplyr)
+ ("r-fastmatch" ,r-fastmatch)
+ ("r-future" ,r-future)
+ ("r-future-apply" ,r-future-apply)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggbio" ,r-ggbio)
+ ("r-ggforce" ,r-ggforce)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggrepel" ,r-ggrepel)
+ ("r-ggseqlogo" ,r-ggseqlogo)
+ ("r-iranges" ,r-iranges)
+ ("r-irlba" ,r-irlba)
+ ("r-lsa" ,r-lsa)
+ ("r-matrix" ,r-matrix)
+ ("r-patchwork" ,r-patchwork)
+ ("r-pbapply" ,r-pbapply)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpproll" ,r-rcpproll)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-scales" ,r-scales)
+ ("r-seurat" ,r-seurat)
+ ("r-seuratobject" ,r-seuratobject)
+ ("r-stringi" ,r-stringi)
+ ("r-tidyr" ,r-tidyr)))
+ (home-page "https://github.com/timoast/signac/")
+ (synopsis
+ "Analysis of Single-Cell Chromatin Data")
+ (description
+ "This package provides a framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart et al. (2020) <doi:10.1101/2020.11.09.373613>.")
+ (license expat))))
+
(define-public r-stringi
(package
(name "r-stringi")
@@ -1851,6 +1910,74 @@ and density estimation.")
times.")
(license license:gpl2)))
+(define-public r-chromstardata
+ (package
+ (name "r-chromstardata")
+ (version "1.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri
+ "chromstaRData"
+ version
+ 'experiment))
+ (sha256
+ (base32
+ "0ph80d53598635bb8g61acg5rqwnj8644a0gh297r4hgbvwlflab"))))
+ (properties `((upstream-name . "chromstaRData")))
+ (build-system r-build-system)
+ (home-page
+ "https://bioconductor.org/packages/chromstaRData")
+ (synopsis
+ "ChIP-seq data for Demonstration Purposes")
+ (description
+ "ChIP-seq data for demonstration purposes in the chromstaR package.")
+ (license gpl3)))
+
+(define-public r-chromstar
+ (let ((commit
+ "16c0394a3a0857a050237d2b8b33cd02d92d6239")
+ (revision "1"))
+ (package
+ (name "r-chromstar")
+ (version (git-version "1.17.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://git.bioconductor.org/packages/chromstaR")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0wr6wlz3z3x21c25hgczalswicrqfhw00wmsa9jjd42w4hj5lkh9"))))
+ (properties `((upstream-name . "chromstaR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bamsignals" ,r-bamsignals)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-chromstardata" ,r-chromstardata)
+ ("r-doparallel" ,r-doparallel)
+ ("r-foreach" ,r-foreach)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-iranges" ,r-iranges)
+ ("r-mvtnorm" ,r-mvtnorm)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)))
+ (native-inputs `(("r-knitr" ,r-knitr)))
+ (home-page
+ "https://git.bioconductor.org/packages/chromstaR")
+ (synopsis
+ "Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data")
+ (description
+ "This package implements functions for combinatorial and differential analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, export to genome browser viewable files, and functi
+ons for enrichment analyses.")
+ (license artistic2.0))))
+
(define-public r-data-table
(package
(name "r-data-table")
--
2.17.1
next reply other threads:[~2021-03-22 10:15 UTC|newest]
Thread overview: 2+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-03-22 10:12 hong li [this message]
2021-03-22 13:39 ` bug#47314: [Patch] two r packages (chromstardata and signac) Ricardo Wurmus
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