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author | Ricardo Wurmus <rekado@elephly.net> | 2022-01-11 14:47:36 +0100 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2022-01-11 14:48:26 +0100 |
commit | 61a1c3f72df3b0333865d6071beaea60294f2ce7 (patch) | |
tree | 4eed30288db0f76378722a158afd5eb891c49676 | |
parent | 81ab20162653cf215d3305086d207472eab6385c (diff) | |
download | guix-61a1c3f72df3b0333865d6071beaea60294f2ce7.tar.gz |
gnu: Add r-transcriptr.
* gnu/packages/bioconductor.scm (r-transcriptr): New variable.
-rw-r--r-- | gnu/packages/bioconductor.scm | 50 |
1 files changed, 50 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6eb34c3793..0fbe0965c2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4472,6 +4472,56 @@ this package. It also provides functionalities for visualizing, summarizing and comparing the clusterings.") (license license:expat))) +(define-public r-transcriptr + (package + (name "r-transcriptr") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "transcriptR" version)) + (sha256 + (base32 "1p5l2z3szx3qh02x7r81ajl7yc5wqsri6q6pzw83livmalcli5yy")))) + (properties `((upstream-name . "transcriptR"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-caret + r-chipseq + r-e1071 + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-iranges + r-proc + r-reshape2 + r-rsamtools + r-rtracklayer + r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/transcriptR") + (synopsis "Primary transcripts detection and quantification") + (description + "The differences in the RNA types being sequenced have an impact on the +resulting sequencing profiles. mRNA-seq data is enriched with reads derived +from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial +broader coverage of both exonic and intronic regions. The presence of +intronic reads in GRO-seq type of data makes it possible to use it to +computationally identify and quantify all de novo continuous regions of +transcription distributed across the genome. This type of data, however, is +more challenging to interpret and less common practice compared to mRNA-seq. +One of the challenges for primary transcript detection concerns the +simultaneous transcription of closely spaced genes, which needs to be properly +divided into individually transcribed units. The R package transcriptR +combines RNA-seq data with ChIP-seq data of histone modifications that mark +active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to +overcome this challenge. The advantage of this approach over the use of, for +example, gene annotations is that this approach is data driven and therefore +able to deal also with novel and case specific events.") + (license license:gpl3))) + (define-public r-trajectoryutils (package (name "r-trajectoryutils") |