recipe bioconductor-casper

Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/casper.html

License

GPL (>=2)

Recipe

/bioconductor-casper/meta.yaml

Links

biotools: casper

package bioconductor-casper

Versions

2.16.0-0, 2.14.0-0, 2.12.0-0, 2.10.0-0

Depends

• bioconductor-biobase >=2.42.0,<2.43.0

• bioconductor-biocgenerics >=0.28.0,<0.29.0

• bioconductor-ebarrays >=2.46.0,<2.47.0

• bioconductor-gaga >=2.28.0,<2.29.0

• bioconductor-genomeinfodb >=1.18.0,<1.19.0

• bioconductor-genomicfeatures >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.34.0,<1.35.0

• bioconductor-iranges >=2.16.0,<2.17.0

• bioconductor-limma >=3.38.0,<3.39.0

• bioconductor-rsamtools >=1.34.0,<1.35.0

• bioconductor-rtracklayer >=1.42.0,<1.43.0

• bioconductor-s4vectors >=0.20.0,<0.21.0

• libgcc-ng >=7.3.0

• libstdcxx-ng >=7.3.0

• r-base >=3.5.1,<3.5.2.0a0

• r-coda

• r-gtools

• r-mgcv

• r-sqldf

• r-survival

• r-vgam

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-casper

and update with:

conda update bioconductor-casper

or use the docker container:

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

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

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-casper/README.html)