ctdR
This is the development version of ctdR; to use it, please install the devel version of Bioconductor.
Enrichment Analysis of Chemical-Gene Interactions from the Comparative Toxicogenomics Database
Bioconductor version: Development (3.24)
Identifies chemicals significantly associated with a set of genes using data from the Comparative Toxicogenomics Database (CTD, <https://ctdbase.org>). Supports four enrichment methods through a unified interface: Over-Representation Analysis (ORA) via a hypergeometric test on stats::phyper(), Gene Set Enrichment Analysis (GSEA) via 'fgsea', the competitive gene-set test CAMERA via 'limma', and per-sample Gene Set Variation Analysis (GSVA) via 'GSVA'. Users download the CTD chemical-gene interactions file once, import it with import_CTD(), and then run enrichment_CTD() on either a gene list (ORA, GSEA) or an expression matrix (CAMERA, GSVA). This package does not bundle or redistribute CTD data. Users must download the required data files directly from <https://ctdbase.org> and comply with the CTD data licensing terms (see <https://ctdbase.org/about/legal.jsp>).
Author: Luigi Corsaro [aut, cre] 
Maintainer: Luigi Corsaro <lcorsaro69 at gmail.com>
citation("ctdR")):Luigi Corsaro. ctdR: Enrichment Analysis of Chemical-Gene Interactions from the Comparative Toxicogenomics Database. doi:10.18129/B9.bioc.ctdR, R package version 0.99.11, https://bioconductor.org/packages/ctdR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("ctdR")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("ctdR")| Introduction to ctdR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Annotation, DataImport, GeneExpression, GeneSetEnrichment, Pathways, Software |
| Version | 0.99.11 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | Apache License 2.0 | file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | fgsea, ggplot2, readr, org.Hs.eg.db, AnnotationDbi, limma, GSVA, stats, BiocIO, BiocFileCache, S4Vectors, SummarizedExperiment, methods |
| System Requirements | |
| URL | https://luigicorsaro.com/ctdR/ https://github.com/drake69/ctdR |
| Bug Reports | https://github.com/drake69/ctdR/issues |
See More
| Suggests | testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ctdR_0.99.11.tar.gz |
| Windows Binary (x86_64) | ctdR_0.99.11.zip |
| macOS Binary (big-sur-x86_64) | ctdR_0.99.11.tgz |
| macOS Binary (sonoma-arm64) | ctdR_0.99.11.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ctdR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ctdR |
| Package Short Url | https://bioconductor.org/packages/ctdR/ |
| Package Downloads Report | Download Stats |