recipe bioconductor-rgreat

GREAT Analysis - Functional Enrichment on Genomic Regions

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-rgreat/meta.yaml

Links:

biotools: rgreat, doi: 10.1038/nmeth.3252

GREAT (Genomic Regions Enrichment of Annotations Tool) is a type of functional enrichment analysis directly performed on genomic regions. This package implements the GREAT algorithm (the local GREAT analysis), also it supports directly interacting with the GREAT web service (the online GREAT analysis). Both analysis can be viewed by a Shiny application. rGREAT by default supports more than 600 organisms and a large number of gene set collections, as well as self-provided gene sets and organisms from users. Additionally, it implements a general method for dealing with background regions.

package bioconductor-rgreat

versions:

2.2.0-0,  2.0.0-1,  2.0.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0, 

2.2.0-0,  2.0.0-1,  2.0.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.14.0-0,  1.12.1-0,  1.11.1-0,  1.8.0-0

depends bioconductor-annotationdbi:

>=1.62.0,<1.63.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicfeatures:

>=1.52.0,<1.53.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-go.db:

>=3.17.0,<3.18.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-org.hs.eg.db:

>=3.17.0,<3.18.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene:

>=3.2.0,<3.3.0

depends bioconductor-txdb.hsapiens.ucsc.hg38.knowngene:

>=3.17.0,<3.18.0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-circlize:

depends r-digest:

depends r-doparallel:

depends r-dt:

depends r-foreach:

depends r-getoptlong:

>=0.0.9

depends r-globaloptions:

depends r-progress:

depends r-rcolorbrewer:

depends r-rcpp:

depends r-rcurl:

depends r-rjson:

depends r-shiny:

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-rgreat

and update with::

   mamba update bioconductor-rgreat

To create a new environment, run:

mamba create --name myenvname bioconductor-rgreat

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-rgreat:<tag>

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

Download stats

Link to this page

Render an 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-rgreat/README.html)