recipe bioconductor-dexseq

Inference of differential exon usage in RNA-Seq

Homepage:

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

License:

GPL (>= 3)

Recipe:

/bioconductor-dexseq/meta.yaml

Links:

biotools: dexseq, usegalaxy-eu: 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.

package bioconductor-dexseq

Versions:

1.44.0-2,  1.40.0-0,  1.38.0-0,  1.36.0-1,  1.36.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.28.1-1, 

1.44.0-2,  1.40.0-0,  1.38.0-0,  1.36.0-1,  1.36.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-1,  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 >=1.60.0,<1.61.0

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-biomart >=2.54.0,<2.55.0

• bioconductor-deseq2 >=1.38.0,<1.39.0

• bioconductor-genefilter >=1.80.0,<1.81.0

• bioconductor-geneplotter >=1.76.0,<1.77.0

• 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-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• htseq >=2.0.2,<2.1

• r-base >=4.2,<4.3.0a0

• r-hwriter

• r-rcolorbrewer

• r-statmod

• r-stringr

Required By:

• bioconductor-diffutr

• trinity

• bioconductor-isoformswitchanalyzer

• bioconductor-interest

• bioconductor-pasilla

Installation

With an activated Bioconda channel (see 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>)

Download stats

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