recipe bioconductor-ctrap

Identification of candidate causal perturbations from differential gene expression data

Homepage

https://bioconductor.org/packages/3.11/bioc/html/cTRAP.html

License

MIT + file LICENSE

Recipe

/bioconductor-ctrap/meta.yaml

Compare differential gene expression results with those from known cellular perturbations (such as gene knock-down, overexpression or small molecules) derived from the Connectivity Map. Such analyses allow not only to infer the molecular causes of the observed difference in gene expression but also to identify small molecules that could drive or revert specific transcriptomic alterations.

package bioconductor-ctrap

Versions

1.6.0-0,  1.4.0-0,  1.2.0-1,  1.0.3-0

Depends

• bioconductor-biomart >=2.44.0,<2.45.0

• bioconductor-fgsea >=1.14.0,<1.15.0

• bioconductor-limma >=3.44.0,<3.45.0

• bioconductor-rhdf5 >=2.32.0,<2.33.0

• r-base >=4.0,<4.1.0a0

• r-cowplot

• r-data.table

• r-dplyr

• r-ggplot2

• r-ggrepel

• r-httr

• r-pbapply

• r-r.utils

• r-readxl

• r-reshape2

Required By

Installation

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

conda install bioconductor-ctrap

and update with:

conda update bioconductor-ctrap

or use the docker container:

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

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

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-ctrap/README.html)