PharmacoGx

This is the released version of PharmacoGx; for the devel version, see PharmacoGx.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4

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 (from within R, enter citation("PharmacoGx")):

Petr Smirnov, Christopher Eeles, Jermiah Joseph, Zhaleh Safikhani, Mark Freeman, Feifei Li, Benjamin Haibe-Kains. PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data. doi:10.18129/B9.bioc.PharmacoGx, R package version 3.16.0, https://bioconductor.org/packages/PharmacoGx.

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")

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	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

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

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, r-universe

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
Package Short Url	https://bioconductor.org/packages/PharmacoGx/
Package Downloads Report	Download Stats