- recipe bioconductor-rgreat
GREAT Analysis - Functional Enrichment on Genomic Regions
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/rGREAT.html
- License:
MIT + file LICENSE
- Recipe:
- 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:
2.4.0-0,2.2.0-0,2.0.0-1,2.0.0-0,1.26.0-0,1.24.0-0,1.22.0-1,1.22.0-0,1.20.0-0,2.4.0-0,2.2.0-0,2.0.0-1,2.0.0-0,1.26.0-0,1.24.0-0,1.22.0-1,1.22.0-0,1.20.0-0,1.18.0-0,1.16.0-1,1.14.0-0,1.12.1-0,1.11.1-0,1.8.0-0- depends bioconductor-annotationdbi:
>=1.64.0,<1.65.0- depends bioconductor-annotationdbi:
>=1.64.1,<1.65.0a0- depends bioconductor-genomeinfodb:
>=1.38.0,<1.39.0- depends bioconductor-genomeinfodb:
>=1.38.1,<1.39.0a0- depends bioconductor-genomicfeatures:
>=1.54.0,<1.55.0- depends bioconductor-genomicfeatures:
>=1.54.1,<1.55.0a0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.1,<1.55.0a0- depends bioconductor-go.db:
>=3.18.0,<3.19.0- depends bioconductor-go.db:
>=3.18.0,<3.19.0a0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0a0- depends bioconductor-org.hs.eg.db:
>=3.18.0,<3.19.0- depends bioconductor-org.hs.eg.db:
>=3.18.0,<3.19.0a0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-s4vectors:
>=0.40.2,<0.41.0a0- depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene:
>=3.2.0,<3.3.0- depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene:
>=3.2.2,<3.3.0a0- depends bioconductor-txdb.hsapiens.ucsc.hg38.knowngene:
>=3.18.0,<3.19.0- depends bioconductor-txdb.hsapiens.ucsc.hg38.knowngene:
>=3.18.0,<3.19.0a0- 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
myenvnamebeing 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:
[](http://bioconda.github.io/recipes/bioconductor-rgreat/README.html)
