This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

cTRAP

This is the development version of cTRAP; for the stable release version, see cTRAP.

Identification of candidate causal perturbations from differential gene expression data

Bioconductor version: Development (3.18)

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 (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, ImmunoOncology, Pathways, RNASeq, Software, Transcriptomics
Version 1.19.0
In Bioconductor since BioC 3.8 (R-3.5) (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
Linking To
Suggests testthat, knitr, covr, rmarkdown, spelling, biomaRt, remotes
System Requirements
Enhances
URL https://nuno-agostinho.github.io/cTRAP https://github.com/nuno-agostinho/cTRAP
Bug Reports https://github.com/nuno-agostinho/cTRAP/issues
See More
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_1.19.0.tar.gz
Windows Binary cTRAP_1.19.0.zip
macOS Binary (x86_64) cTRAP_1.19.0.tgz
macOS Binary (arm64) cTRAP_1.19.0.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