cTRAP
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see cTRAP.
Identification of candidate causal perturbations from differential gene expression data
Bioconductor version: 3.10
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("cTRAP")):
Installation
To install this package, start R (version "3.6") 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")| cTRAP: DGE comparison with cellular perturbations | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, ImmunoOncology, Pathways, RNASeq, Software, Transcriptomics |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.6.0) |
| Imports | biomaRt, cowplot, data.table, dplyr, fgsea, ggplot2, ggrepel, graphics, httr, limma, methods, pbapply, R.utils, readxl, reshape2, rhdf5, stats, tools, utils |
| System Requirements | |
| URL | https://github.com/nuno-agostinho/cTRAP |
| Bug Reports | https://github.com/nuno-agostinho/cTRAP/issues |
See More
| Suggests | testthat, knitr, covr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | cTRAP_1.4.0.tar.gz |
| Windows Binary | cTRAP_1.4.0.zip |
| Mac OS X 10.11 (El Capitan) | cTRAP_1.4.0.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 |
| Old Source Packages for BioC 3.10 | Source Archive |