PharmacoGx
This is the released version of PharmacoGx; for the devel version, see PharmacoGx.
Analysis of Large-Scale Pharmacogenomic Data
Bioconductor version: Release (3.23)
Contains a set of functions to perform large-scale analysis of pharmaco-genomic data. These include the PharmacoSet object for storing the results of pharmacogenomic experiments, as well as a number of functions for computing common summaries of drug-dose response and correlating them with the molecular features in a cancer cell-line.
Author: Petr Smirnov [aut], Christopher Eeles [aut], Jermiah Joseph [aut], Zhaleh Safikhani [aut], Mark Freeman [aut], Feifei Li [aut], Benjamin Haibe-Kains [aut, cre]
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains at utoronto.ca>
citation("PharmacoGx")):
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("PharmacoGx")
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("PharmacoGx")| Creating a PharmacoSet Object | HTML | R Script |
| Detecting Drug Synergy and Antagonism with PharmacoGx 3.0+ | HTML | R Script |
| PharmacoGx: An R Package for Analysis of Large Pharmacogenomic Datasets | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, GeneExpression, Pharmacogenetics, Pharmacogenomics, Software |
| Version | 3.16.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (10 years) |
| License | GPL (>= 3) |
| Depends | R (>= 4.1.0), CoreGx |
| Imports | BiocGenerics, Biobase, S4Vectors, SummarizedExperiment, MultiAssayExperiment, BiocParallel, ggplot2, RColorBrewer, magicaxis, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, reshape2, jsonlite, data.table, checkmate, boot, coop |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/bhklab/PharmacoGx/issues |
See More
| Suggests | pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown, BiocStyle, R.utils |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | gDRimport, Xeva |
| Suggests Me | ToxicoGx |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | PharmacoGx_3.16.0.tar.gz |
| Windows Binary (x86_64) | PharmacoGx_3.16.0.zip |
| macOS Binary (big-sur-x86_64) | PharmacoGx_3.16.0.tgz |
| macOS Binary (sonoma-arm64) | PharmacoGx_3.16.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/PharmacoGx |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/PharmacoGx |
| Bioc Package Browser | https://code.bioconductor.org/browse/PharmacoGx/ |
| Package Short Url | https://bioconductor.org/packages/PharmacoGx/ |
| Package Downloads Report | Download Stats |