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| author | Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> | 2023-11-06 12:06:42 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2023-11-13 15:00:48 +0100 |
| commit | 77025bd51139c74d572299f4b7b33e071cd54cd8 (patch) | |
| tree | 4c6c1022f2dbf791e75b400263126f0b89f8640b /gnu/packages | |
| parent | 4e1c6f499880e867d162dacff32c59635e675dbf (diff) | |
gnu: Add r-basicstarrseq.
* gnu/packages/bioconductor.scm (r-basicstarrseq): New variable.
Change-Id: I88f314877ea4ab98976820a4acc337ae3a34e604
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 35 |
1 files changed, 35 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3955f04bf1..cf7e1c07ac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -22672,6 +22672,41 @@ Additionally, BASiCS can compare gene expression patterns between two or more pre-specified 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") |