recipe bioconductor-ebseq

An R package for gene and isoform differential expression analysis of RNA-seq data

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/EBSeq.html

License:

Artistic-2.0

Recipe:

/bioconductor-ebseq/meta.yaml

Links:

biotools: ebseq, doi: 10.1093/bioinformatics/btt087

Differential Expression analysis at both gene and isoform level using RNA-seq data

package bioconductor-ebseq

versions:

2.4.0-0,  2.0.0-3,  2.0.0-2,  2.0.0-1,  2.0.0-0,  1.40.0-0,  1.38.0-0,  1.34.0-0,  1.32.0-0, 

2.4.0-0,  2.0.0-3,  2.0.0-2,  2.0.0-1,  2.0.0-0,  1.40.0-0,  1.38.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.1-0,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

depends r-bh:

depends r-blockmodeling:

depends r-gplots:

depends r-rcpp:

>=0.12.11

depends r-rcppeigen:

>=0.3.2.9.0

depends r-testthat:

requirements:

additional platforms:

linux-aarch64

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-ebseq

and update with::

   mamba update bioconductor-ebseq

To create a new environment, run:

mamba create --name myenvname bioconductor-ebseq

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-ebseq:<tag>

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

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