recipe bioconductor-loci2path

Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/loci2path.html

License:

Artistic-2.0

Recipe:

/bioconductor-loci2path/meta.yaml

loci2path performs statistics-rigorous enrichment analysis of eQTLs in genomic regions of interest. Using eQTL collections provided by the Genotype-Tissue Expression (GTEx) project and pathway collections from MSigDB.

package bioconductor-loci2path

(downloads) docker_bioconductor-loci2path

versions:
1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0, 

1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.2.0-1,  1.2.0-0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-pheatmap:

depends r-rcolorbrewer:

depends r-wordcloud:

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-loci2path

and update with::

   mamba update bioconductor-loci2path

To create a new environment, run:

mamba create --name myenvname bioconductor-loci2path

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-loci2path:<tag>

(see `bioconductor-loci2path/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-loci2path/README.html)