recipe bioconductor-dexseq

Inference of differential exon usage in RNA-Seq

Homepage:

https://bioconductor.org/packages/3.18/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:

1.48.0-2,  1.48.0-1,  1.48.0-0,  1.46.0-0,  1.44.0-2,  1.40.0-0,  1.38.0-0,  1.36.0-1,  1.36.0-0, 

1.48.0-2,  1.48.0-1,  1.48.0-0,  1.46.0-0,  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:

>=1.64.0,<1.65.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-genefilter:

>=1.84.0,<1.85.0

depends bioconductor-geneplotter:

>=1.80.0,<1.81.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends htseq:

>=2.0.2,<2.1

depends r-base:

>=4.3,<4.4.0a0

depends r-hwriter:

depends r-rcolorbrewer:

depends r-statmod:

depends r-stringr:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-dexseq

and update with::

   mamba update bioconductor-dexseq

To create a new environment, run:

mamba create --name myenvname bioconductor-dexseq

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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