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, ). 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 and comply with the CTD data licensing terms (see ).

Author: Luigi Corsaro [aut, cre] ORCID: 0000-0003-1218-230X

Maintainer: Luigi Corsaro <lcorsaro69 at gmail.com>

Citation (from within R, enter citation("ctdR")):

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

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	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

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 (>= 4.6.0)
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

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

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
Bioc Package Browser	https://code.bioconductor.org/browse/ctdR/
Package Short Url	https://bioconductor.org/packages/ctdR/
Package Downloads Report	Download Stats