recipe bioconductor-dexseq

The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.

Homepage

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

License

GPL (>= 3)

Recipe

/bioconductor-dexseq/meta.yaml

Links

biotools: dexseq

package bioconductor-dexseq

(downloads) docker_bioconductor-dexseq

Versions

1.28.1-1, 1.28.1-0, 1.28.0-0, 1.26.0-2, 1.26.0-1, 1.26.0-0, 1.24.0-3, 1.24.0-1, 1.24.0-0, 1.22.0-0, 1.20.1-2, 1.20.1-1, 1.20.1-0, 1.18.4-1, 1.16.6-0

Depends bioconductor-annotationdbi

>=1.44.0,<1.45.0

Depends bioconductor-biobase

>=2.42.0,<2.43.0

Depends bioconductor-biocgenerics

>=0.28.0,<0.29.0

Depends bioconductor-biocparallel

>=1.16.0,<1.17.0

Depends bioconductor-biomart

>=2.38.0,<2.39.0

Depends bioconductor-deseq2

>=1.22.0,<1.23.0

Depends bioconductor-genefilter

>=1.64.0,<1.65.0

Depends bioconductor-geneplotter

>=1.60.0,<1.61.0

Depends bioconductor-genomicranges

>=1.34.0,<1.35.0

Depends bioconductor-iranges

>=2.16.0,<2.17.0

Depends bioconductor-rsamtools

>=1.34.0,<1.35.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends bioconductor-summarizedexperiment

>=1.12.0,<1.13.0

Depends htseq

>=0.6.1,<0.10.0

Depends python

<3

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-hwriter

Depends r-rcolorbrewer

Depends r-statmod

Depends r-stringr

Requirements

Installation

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

conda install bioconductor-dexseq

and update with:

conda update bioconductor-dexseq

or use the docker container:

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

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