PharmacoGx

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see PharmacoGx.

Analysis of Large-Scale Pharmacogenomic Data

Bioconductor version: 3.14

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], Zhaleh Safikhani [aut], Christopher Eeles [aut], Mark Freeman [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 "4.1") 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 PDF R Script

PharmacoGx: An R Package for Analysis of Large Pharmacogenomic Datasets PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Classification, GeneExpression, Pharmacogenetics, Pharmacogenomics, Software

Version 2.6.0

In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)

License Artistic-2.0

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, glue, checkmate

System Requirements

URL

Bug Reports https://github.com/bhklab/PharmacoGx/issues

Suggests pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown

Linking To

Enhances

Depends On Me

Imports Me 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_2.6.0.tar.gz

Windows Binary PharmacoGx_2.6.0.zip

macOS 10.13 (High Sierra) PharmacoGx_2.6.0.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 3.14 Source Archive