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[bug#66966] [PATCH 06/13] gnu: Add r-basicstarrseq.
From: |
Mădălin Ionel Patrașcu |
Subject: |
[bug#66966] [PATCH 06/13] gnu: Add r-basicstarrseq. |
Date: |
Mon, 6 Nov 2023 12:06:42 +0100 |
* gnu/packages/bioconductor.scm (r-basicstarrseq): New variable.
Change-Id: I88f314877ea4ab98976820a4acc337ae3a34e604
---
gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++
1 file changed, 33 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 184972afb5..986227ec38 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -22358,6 +22358,39 @@ (define-public r-basics
groups of cells.")
(license license:gpl3)))
+(define-public r-basicstarrseq
+ (package
+ (name "r-basicstarrseq")
+ (version "1.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BasicSTARRseq" version))
+ (sha256
+ (base32 "1dw6bv1qk2bn0l3m458sqgvm3s1karh4n3431pl7r0jj2r3mr6xa"))))
+ (properties `((upstream-name . "BasicSTARRseq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-genomeinfodb
+ r-genomicalignments
+ r-genomicranges
+ r-iranges
+ r-s4vectors))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/BasicSTARRseq")
+ (synopsis "Basic peak calling on STARR-seq data")
+ (description
+ "This package implements a method that aims to identify enhancers on large
+scale. The STARR-seq data consists of two sequencing datasets of the same
targets
+in a specifc genome. The input sequences show which regions where tested for
+enhancers. Significant enriched peaks i.e. a lot more sequences in one region
+than in the input where enhancers in the genomic DNA are, can be identified.
So
+the approach pursued is to call peak every region in which there is a lot more
+(significant in a binomial model) STARR-seq signal than input signal and
propose
+an enhancer at that very same position. Enhancers then are called weak or
strong
+dependent of there degree of enrichment in comparison to input.")
+ (license license:lgpl3)))
+
(define-public r-basilisk-utils
(package
(name "r-basilisk-utils")
--
2.41.0
- [bug#66966] [PATCH 02/13] gnu: Add r-bags., (continued)
- [bug#66966] [PATCH 02/13] gnu: Add r-bags., Mădălin Ionel Patrașcu, 2023/11/06
- [bug#66966] [PATCH 10/13] gnu: Add r-bb., Mădălin Ionel Patrașcu, 2023/11/06
- [bug#66966] [PATCH 04/13] gnu: Add r-basic4cseq., Mădălin Ionel Patrașcu, 2023/11/06
- [bug#66966] [PATCH 07/13] gnu: Add r-bayesknockdown., Mădălin Ionel Patrașcu, 2023/11/06
- [bug#66966] [PATCH 11/13] gnu: Add r-baynorm., Mădălin Ionel Patrașcu, 2023/11/06
- [bug#66966] [PATCH 13/13] gnu: Add r-bcrank., Mădălin Ionel Patrașcu, 2023/11/06
- [bug#66966] [PATCH 09/13] gnu: Add r-bayesspace., Mădălin Ionel Patrașcu, 2023/11/06
- [bug#66966] [PATCH 08/13] gnu: Add r-rcppdist., Mădălin Ionel Patrașcu, 2023/11/06
- [bug#66966] [PATCH 12/13] gnu: Add r-bbcanalyzer., Mădălin Ionel Patrașcu, 2023/11/06
- [bug#66966] [PATCH 03/13] gnu: Add r-bsgenome-ecoli-ncbi-20080805., Mădălin Ionel Patrașcu, 2023/11/06
- [bug#66966] [PATCH 06/13] gnu: Add r-basicstarrseq.,
Mădălin Ionel Patrașcu <=
- bug#66966: [PATCH 01/13] gnu: Add r-breastcancervdx., Ricardo Wurmus, 2023/11/13