recipe bioconductor-compgo

This package contains functions to accomplish several tasks. It is able to download full genome databases from UCSC, import .bed files easily, annotate these .bed file regions with genes (plus distance) from aforementioned database dumps, interface with DAVID to create functional annotation and gene ontology enrichment charts based on gene lists (such as those generated from input .bed files) and finally visualise and compare these enrichments using either directed acyclic graphs or scatterplots.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/CompGO.html

License

GPL-2

Recipe

/bioconductor-compgo/meta.yaml

package bioconductor-compgo

(downloads) docker_bioconductor-compgo

Versions

1.18.0-0

Depends bioconductor-genomicfeatures

>=1.34.0,<1.35.0

Depends bioconductor-pathview

>=1.22.0,<1.23.0

Depends bioconductor-pcamethods

>=1.74.0,<1.75.0

Depends bioconductor-rdavidwebservice

>=1.20.0,<1.21.0

Depends bioconductor-rgraphviz

>=2.26.0,<2.27.0

Depends bioconductor-rtracklayer

>=1.42.0,<1.43.0

Depends bioconductor-txdb.mmusculus.ucsc.mm9.knowngene

>=3.2.0,<3.3.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-ggplot2

Depends r-reshape2

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-compgo

and update with:

conda update bioconductor-compgo

or use the docker container:

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

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