Package Recipe 'bioconductor-casper'

recipe bioconductor-casper

Characterization of Alternative Splicing based on Paired-End Reads

Homepage: https://bioconductor.org/packages/3.14/bioc/html/casper.html
License: GPL (>=2)
Recipe: /bioconductor-casper/meta.yaml

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.

package bioconductor-casper¶

Versions

2.28.0-1, 2.28.0-0, 2.26.0-0, 2.23.0-0, 2.22.0-0, 2.20.0-0, 2.18.0-1, 2.16.0-0, 2.14.0-0,

2.28.0-1, 2.28.0-0, 2.26.0-0, 2.23.0-0, 2.22.0-0, 2.20.0-0, 2.18.0-1, 2.16.0-0, 2.14.0-0, 2.12.0-0, 2.10.0-0

Depends

bioconductor-biobase >=2.54.0,<2.55.0
bioconductor-biocgenerics >=0.40.0,<0.41.0
bioconductor-ebarrays >=2.58.0,<2.59.0
bioconductor-gaga >=2.40.0,<2.41.0
bioconductor-genomeinfodb >=1.30.0,<1.31.0
bioconductor-genomicfeatures >=1.46.0,<1.47.0
bioconductor-genomicranges >=1.46.0,<1.47.0
bioconductor-iranges >=2.28.0,<2.29.0
bioconductor-limma >=3.50.0,<3.51.0
bioconductor-rsamtools >=2.10.0,<2.11.0
bioconductor-rtracklayer >=1.54.0,<1.55.0
bioconductor-s4vectors >=0.32.0,<0.33.0
libblas >=3.8.0,<4.0a0
libgcc-ng >=10.3.0
liblapack >=3.8.0,<4.0a0
libstdcxx-ng >=10.3.0
r-base >=4.1,<4.2.0a0
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>)

Download stats¶

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)