recipe bioconductor-fgsea

Fast Gene Set Enrichment Analysis

Homepage:

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

License:

MIT + file LICENCE

Recipe:

/bioconductor-fgsea/meta.yaml

Links:

biotools: fgsea, doi: 10.1101/060012

The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.

package bioconductor-fgsea

versions:

1.32.2-0,  1.32.0-0,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.20.0-2,  1.20.0-1, 

1.32.2-0,  1.32.0-0,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.20.0-2,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.1-0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0a0

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-cowplot:

depends r-data.table:

depends r-fastmatch:

depends r-ggplot2:

>=2.2.0

depends r-matrix:

depends r-rcpp:

depends r-scales:

requirements:

additional platforms:

linux-aarch64,  osx-arm64

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-fgsea

and update with::

   mamba update bioconductor-fgsea

To create a new environment, run:

mamba create --name myenvname bioconductor-fgsea

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-fgsea:<tag>

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

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