recipe bioconductor-rgreat

GREAT Analysis - Functional Enrichment on Genomic Regions

Homepage:

https://bioconductor.org/packages/3.16/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:

2.0.0-1,  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, 

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 >=1.60.0,<1.61.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicfeatures >=1.50.0,<1.51.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-go.db >=3.16.0,<3.17.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-org.hs.eg.db >=3.16.0,<3.17.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0

• bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.16.0,<3.17.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-base >=4.2,<4.3.0a0

• r-circlize

• r-digest

• r-doparallel

• r-dt

• r-foreach

• r-getoptlong >=0.0.9

• r-globaloptions

• r-progress

• r-rcolorbrewer

• r-rcpp

• r-rcurl

• r-rjson

• r-shiny

Required By:

• bioconductor-ataccogaps

• bioconductor-profileplyr

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-rgreat

and update with:

conda update bioconductor-rgreat

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-rgreat:<tag>

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

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