recipe bioconductor-diffutr

diffUTR: Streamlining differential exon and 3' UTR usage

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/diffUTR.html

License:

GPL-3

Recipe:

/bioconductor-diffutr/meta.yaml

The diffUTR package provides a uniform interface and plotting functions for limma/edgeR/DEXSeq -powered differential bin/exon usage. It includes in addition an improved version of the limma::diffSplice method. Most importantly, diffUTR further extends the application of these frameworks to differential UTR usage analysis using poly-A site databases.

package bioconductor-diffutr

versions:

1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-complexheatmap:

>=2.16.0,<2.17.0

depends bioconductor-dexseq:

>=1.46.0,<1.47.0

depends bioconductor-edger:

>=3.42.0,<3.43.0

depends bioconductor-ensembldb:

>=2.24.0,<2.25.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-limma:

>=3.56.0,<3.57.0

depends bioconductor-rsubread:

>=2.14.0,<2.15.0

depends bioconductor-rtracklayer:

>=1.60.0,<1.61.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-ggplot2:

depends r-ggrepel:

depends r-matrixstats:

depends r-stringi:

depends r-viridislite:

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-diffutr

and update with::

   mamba update bioconductor-diffutr

To create a new environment, run:

mamba create --name myenvname bioconductor-diffutr

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-diffutr:<tag>

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

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Link to this page

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