PharmacoGx
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see PharmacoGx.
Analysis of Large-Scale Pharmacogenomic Data
Bioconductor version: 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("PharmacoGx")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | Classification, GeneExpression, Pharmacogenetics, Pharmacogenomics, Software |
| Version | 3.8.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (8 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 | Xeva, gDRimport |
| 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_3.8.0.tar.gz |
| Windows Binary (x86_64) | PharmacoGx_3.8.0.zip |
| macOS Binary (x86_64) | PharmacoGx_3.8.0.tgz |
| macOS Binary (arm64) | PharmacoGx_3.8.0.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 |