cTRAP
Identification of candidate causal perturbations from differential gene expression data
Bioconductor version: 3.24 · Package version: 1.31.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("cTRAP")Details
| Maintainer | Nuno Saraiva-Agostinho <nunodanielagostinho@gmail.com> |
| Author | Bernardo P. de Almeida [aut], Nuno Saraiva-Agostinho [aut, cre], Nuno L. Barbosa-Morais [aut, led] |
| License | MIT + file LICENSE |
| URL | https://nuno-agostinho.github.io/cTRAP, https://github.com/nuno-agostinho/cTRAP |
| Bug Reports | https://github.com/nuno-agostinho/cTRAP/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, ImmunoOncology, Pathways, RNASeq, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/cTRAP/ |
Citation
From within R, enter citation("cTRAP"):
Bernardo P. de Almeida, Nuno Saraiva-Agostinho, Nuno L. Barbosa-Morais. cTRAP: Identification of candidate causal perturbations from differential gene expression data. doi:10.18129/B9.bioc.cTRAP, R package version 1.31.0, https://bioconductor.org/packages/cTRAP.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | cTRAP_1.31.0.tar.gz |
| Windows binary (x86_64) | cTRAP_1.31.0.zip |
| macOS binary (arm64) | cTRAP_1.31.0.tgz |
| macOS binary (x86_64) | cTRAP_1.31.0.tgz |
Dependencies
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, qs2, R.utils, readxl, reshape2, rhdf5, rlang, scales, shiny (>= 1.7.0), shinycssloaders, stats, tibble, tools, utils
Suggests: testthat, knitr, covr, rmarkdown, spelling, biomaRt, remotes