From: "Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
To: <51464@debbugs.gnu.org>
Cc: rekado@elephly.net,
"Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
Subject: [bug#51464] [PATCH 2/2] gnu: Add r-xnastring.
Date: Thu, 28 Oct 2021 20:26:09 +0200 [thread overview]
Message-ID: <20211028182609.1880-2-madalinionel.patrascu@mdc-berlin.de> (raw)
In-Reply-To: <20211028182609.1880-1-madalinionel.patrascu@mdc-berlin.de>
* gnu/packages/bioconductor.scm (r-xnastring): New variable.
---
gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++
1 file changed, 44 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 90a0e1f288..abb5b7065d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4627,6 +4627,50 @@ (define-public r-vsn
and specific in detecting differential transcription.")
(license license:artistic2.0)))
+(define-public r-xnastring
+ (package
+ (name "r-xnastring")
+ (version "1.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "XNAString" version))
+ (sha256
+ (base32 "1rpcvn54a6s3iwmdg96rshilr1mqcb1nlbvzbyp5xi55km7iwm8i"))))
+ (properties `((upstream-name . "XNAString")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-data-table" ,r-data-table)
+ ("r-formattable" ,r-formattable)
+ ("r-future-apply" ,r-future-apply)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-htmltools" ,r-htmltools)
+ ("r-htmlwidgets" ,r-htmlwidgets)
+ ("r-iranges" ,r-iranges)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-stringi" ,r-stringi)
+ ("r-stringr" ,r-stringr)))
+ (native-inputs `(("r-knitr" ,r-knitr)))
+ (home-page "https://git.bioconductor.org/packages/XNAString")
+ (synopsis "Manipulation of modified oligonucleotide sequences")
+ (description
+ "The R @code{XNAString} package allows for description of base sequences
+and associated chemical modifications in a single object. XNAString is able to
+capture single stranded, as well as double stranded molecules. Chemical
+modifications are represented as independent strings associated with different
+features of the molecules (base sequence, sugar sequence, backbone sequence,
+modifications) and can be read or written to a @dfn{Hierarchical Editing
+Language for Macromolecules} (HELM) notation. It also enables secondary
+structure prediction using RNAfold from ViennaRNA. XNAString is designed to be
+efficient representation of nucleic-acid based therapeutics, therefore it
+stores information about target sequences and provides interface for matching
+and alignment functions from Biostrings package.")
+ (license license:gpl2)))
+
(define-public r-xvector
(package
(name "r-xvector")
--
2.33.0
next prev parent reply other threads:[~2021-10-28 18:27 UTC|newest]
Thread overview: 5+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-10-28 18:24 [bug#51464] Add r-xnastring (bioconductor) and r-formattable (cran) MadalinIonel.Patrascu
2021-10-28 18:26 ` [bug#51464] [PATCH 1/2] gnu: Add r-formattable Mădălin Ionel Patrașcu
2021-10-28 18:26 ` Mădălin Ionel Patrașcu [this message]
2021-10-30 19:52 ` [bug#51464] Add r-xnastring (bioconductor) and r-formattable (cran) Ricardo Wurmus
2021-11-27 20:23 ` bug#51464: " Ricardo Wurmus
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