PharmacoGx

DOI: 10.18129/B9.bioc.PharmacoGx    

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

Analysis of Large-Scale Pharmacogenomic Data

Bioconductor version: Development (3.13)

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 (!requireNamespace("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")

 

PDF R Script Creating a PharmacoSet Object
PDF 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 2.3.0
In Bioconductor since BioC 3.4 (R-3.3) (4 years)
License Artistic-2.0
Depends R (>= 3.6), CoreGx
Imports Biobase, S4Vectors, SummarizedExperiment, BiocParallel, ggplot2, magicaxis, RColorBrewer, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, reshape2, jsonlite, data.table
LinkingTo
Suggests pander, rmarkdown, knitr, knitcitations, crayon, testthat, BiocGenerics
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_2.3.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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

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