cTRAP

DOI: 10.18129/B9.bioc.cTRAP  

Identification of candidate causal perturbations from differential gene expression data

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cTRAP")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("cTRAP")

 

HTML	R Script	cTRAP: identifying candidate causal perturbations from differential gene expression data
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DifferentialExpression, GeneExpression, GeneSetEnrichment, ImmunoOncology, Pathways, RNASeq, Software, Transcriptomics
Version	1.16.0
In Bioconductor since	BioC 3.8 (R-3.5) (4.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.0)
Imports	AnnotationDbi, AnnotationHub, binr, cowplot, data.table, dplyr, DT, fastmatch, fgsea, ggplot2, ggrepel, graphics, highcharter, htmltools, httr, limma, methods, parallel, pbapply, purrr, qs, R.utils, readxl, reshape2, rhdf5, rlang, scales, shiny (>= 1.7.0), shinycssloaders, stats, tibble, tools, utils
LinkingTo
Suggests	testthat, knitr, covr, rmarkdown, spelling, biomaRt, remotes
SystemRequirements
Enhances
URL	https://nuno-agostinho.github.io/cTRAP 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_1.16.0.tar.gz
Windows Binary	cTRAP_1.16.0.zip
macOS Binary (x86_64)	cTRAP_1.16.0.tgz
macOS Binary (arm64)	cTRAP_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/cTRAP
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/cTRAP
Bioc Package Browser	https://code.bioconductor.org/browse/cTRAP/
Package Short Url	https://bioconductor.org/packages/cTRAP/
Package Downloads Report	Download Stats