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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")