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PharmacoGx

This is the development version of PharmacoGx; for the stable release version, see PharmacoGx.

Analysis of Large-Scale Pharmacogenomic Data


Bioconductor version: Development (3.19)

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")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Classification, GeneExpression, Pharmacogenetics, Pharmacogenomics, Software
Version 3.7.2
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL (>= 3)
Depends R (>= 3.6), 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_3.7.2.tar.gz
Windows Binary PharmacoGx_3.7.2.zip
macOS Binary (x86_64) PharmacoGx_3.7.2.tgz
macOS Binary (arm64) PharmacoGx_3.7.2.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