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PharmacoGx
This is thereleased version of PharmacoGx; for the devel version, seePharmacoGx.
Analysis of Large-Scale Pharmacogenomic Data
Bioconductor version: Release (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("PharmacoGx")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("PharmacoGx")For older versions of R, please refer to the appropriateBioconductor 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 | 3.14.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (9 years) |
| License | GPL (>= 3) |
| Depends | R (>= 4.1.0),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
FollowInstallation instructions to use this package in your R session.
| Source Package | PharmacoGx_3.14.0.tar.gz |
| Windows Binary (x86_64) | PharmacoGx_3.14.0.zip (64-bit only) |
| macOS Binary (x86_64) | PharmacoGx_3.14.0.tgz |
| macOS Binary (arm64) | PharmacoGx_3.14.0.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 |