ToxicoGx
This is the released version of ToxicoGx; for the devel version, see ToxicoGx.
Analysis of Large-Scale Toxico-Genomic Data
Bioconductor version: Release (3.23)
Contains a set of functions to perform large-scale analysis of toxicogenomic data, providing a standardized data structure to hold information relevant to annotation, visualization and statistical analysis of toxicogenomic data.
Author: Sisira Nair [aut], Esther Yoo [aut], Christopher Eeles [aut], Amy Tang [aut], Nehme El-Hachem [aut], Petr Smirnov [aut], Jermiah Joseph [aut], Benjamin Haibe-Kains [aut, cre]
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains at utoronto.ca>
citation("ToxicoGx")):
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")
BiocManager::install("ToxicoGx")
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("ToxicoGx")| ToxicoGx: An R Platform for Integrated Toxicogenomics Data Analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, Pharmacogenetics, Pharmacogenomics, Software |
| Version | 2.16.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1), CoreGx |
| Imports | SummarizedExperiment, BiocGenerics, S4Vectors, Biobase, BiocParallel, ggplot2, tibble, dplyr, caTools, downloader, magrittr, methods, reshape2, tidyr, data.table, assertthat, scales, graphics, grDevices, parallel, stats, utils, limma, jsonlite |
| System Requirements | |
| URL |
See More
| Suggests | rmarkdown, testthat, BiocStyle, knitr, tinytex, devtools, PharmacoGx, xtable, markdown |
| 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 | ToxicoGx_2.16.0.tar.gz |
| Windows Binary (x86_64) | ToxicoGx_2.16.0.zip |
| macOS Binary (big-sur-x86_64) | ToxicoGx_2.16.0.tgz |
| macOS Binary (sonoma-arm64) | ToxicoGx_2.16.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ToxicoGx |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ToxicoGx |
| Bioc Package Browser | https://code.bioconductor.org/browse/ToxicoGx/ |
| Package Short Url | https://bioconductor.org/packages/ToxicoGx/ |
| Package Downloads Report | Download Stats |