recipe bioconductor-sgseq

Splice event prediction and quantification from RNA-seq data

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/SGSeq.html

License:

Artistic-2.0

Recipe:

/bioconductor-sgseq/meta.yaml

Links:

biotools: sgseq

SGSeq is a software package for analyzing splice events from RNA-seq data. Input data are RNA-seq reads mapped to a reference genome in BAM format. Genes are represented as a splice graph, which can be obtained from existing annotation or predicted from the mapped sequence reads. Splice events are identified from the graph and are quantified locally using structurally compatible reads at the start or end of each splice variant. The software includes functions for splice event prediction, quantification, visualization and interpretation.

package bioconductor-sgseq

Versions:

1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.16.2-0, 

1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.16.2-0,  1.14.0-0,  1.12.0-0,  1.10.0-0

Depends:

• bioconductor-annotationdbi >=1.60.0,<1.61.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicalignments >=1.34.0,<1.35.0

• bioconductor-genomicfeatures >=1.50.0,<1.51.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-igraph

• r-runit

Required By:

• bioconductor-eventpointer

• bioconductor-rhisat2

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-sgseq

and update with:

conda update bioconductor-sgseq

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-sgseq:<tag>

(see bioconductor-sgseq/tags for valid values for <tag>)

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