PharmacoGx

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

Analysis of Large-Scale Pharmacogenomic Data

Bioconductor version: Development (3.22)

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 "4.5") 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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, GeneExpression, Pharmacogenetics, Pharmacogenomics, Software
Version	3.13.0
In Bioconductor since	BioC 3.4 (R-3.3) (8.5 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

Suggests	pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown, BiocStyle, R.utils
Linking To	Rcpp
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
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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