recipe bioconductor-rsubread

Mapping, quantification and variant analysis of sequencing data

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/Rsubread.html

License:

GPL (>=3)

Recipe:

/bioconductor-rsubread/meta.yaml

Links:

biotools: rsubread

Alignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads.

package bioconductor-rsubread

versions:

2.20.0-0,  2.16.1-0,  2.16.0-0,  2.14.2-0,  2.12.0-1,  2.12.0-0,  2.8.2-0,  2.8.1-0,  2.8.0-0, 

2.20.0-0,  2.16.1-0,  2.16.0-0,  2.14.2-0,  2.12.0-1,  2.12.0-0,  2.8.2-0,  2.8.1-0,  2.8.0-0,  2.6.1-0,  2.4.3-0,  2.4.0-0,  2.2.1-0,  2.0.0-0,  1.34.6-0,  1.34.4-0,  1.34.0-0,  1.32.4-0,  1.32.2-0,  1.30.9-0,  1.28.1-0,  1.28.0-0,  1.26.1-0,  1.25.2-0,  1.23.0-0,  1.22.1-0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libzlib:

>=1.3.1,<2.0a0

depends r-base:

>=4.4,<4.5.0a0

depends r-matrix:

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-rsubread

and update with::

   mamba update bioconductor-rsubread

To create a new environment, run:

mamba create --name myenvname bioconductor-rsubread

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-rsubread:<tag>

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

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