cTRAP

DOI: 10.18129/B9.bioc.cTRAP    

Identification of candidate causal perturbations from differential gene expression data

Bioconductor version: Release (3.8)

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.

Author: Bernardo P. de Almeida [aut], Nuno Saraiva-Agostinho [aut, cre], Nuno L. Barbosa-Morais [aut, led]

Maintainer: Nuno Saraiva-Agostinho <nunodanielagostinho at gmail.com>

Citation (from within R, enter citation("cTRAP")):

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("cTRAP", version = "3.8")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("cTRAP")

 

HTML R Script cTRAP: DGE comparison with cellular perturbations
PDF   Reference Manual
Text   LICENSE

Details

biocViews DifferentialExpression, GeneExpression, Pathways, RNASeq, Software, Transcriptomics
Version 1.0.1
License MIT + file LICENSE
Depends R (>= 3.5.0)
Imports data.table, limma, stats, fgsea, pbapply, plyr, cowplot, ggplot2, rhdf5, R.utils, httr, methods, piano, readr, utils, graphics
LinkingTo
Suggests testthat, knitr, covr, biomaRt
SystemRequirements
Enhances
URL https://github.com/nuno-agostinho/cTRAP
BugReports https://github.com/nuno-agostinho/cTRAP/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package cTRAP_1.0.1.tar.gz
Windows Binary cTRAP_1.0.1.zip
Mac OS X 10.11 (El Capitan) cTRAP_1.0.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/cTRAP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cTRAP
Package Short Url http://bioconductor.org/packages/cTRAP/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.8 Source Archive

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