PharmacoGx

DOI: 10.18129/B9.bioc.PharmacoGx  

Analysis of Large-Scale Pharmacogenomic Data

Bioconductor version: Release (3.17)

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], Zhaleh Safikhani [aut], Mark Freeman [aut], Feifei Li [aut], Jermiah Joseph [aut], Benjamin Haibe-Kains [aut, cre]

Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains at utoronto.ca>

Installation

To install this package, start R (version "4.3") 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")

 

HTML	R Script	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
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, GeneExpression, Pharmacogenetics, Pharmacogenomics, Software
Version	3.4.0
In Bioconductor since	BioC 3.4 (R-3.3) (7 years)
License	GPL (>= 3)
Depends	R (>= 3.6), CoreGx
Imports	BiocGenerics, Biobase, S4Vectors, SummarizedExperiment, MultiAssayExperiment, BiocParallel, ggplot2, magicaxis, RColorBrewer, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, reshape2, jsonlite, data.table, checkmate, boot, coop
LinkingTo	Rcpp
Suggests	pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown, BiocStyle, R.utils
SystemRequirements
Enhances
URL
BugReports	https://github.com/bhklab/PharmacoGx/issues
Depends On Me
Imports Me	Xeva
Suggests Me	ToxicoGx
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	PharmacoGx_3.4.0.tar.gz
Windows Binary	PharmacoGx_3.4.0.zip
macOS Binary (x86_64)	PharmacoGx_3.4.0.tgz
macOS Binary (arm64)	PharmacoGx_3.4.0.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
Old Source Packages for BioC 3.17	Source Archive