cmapR

DOI: 10.18129/B9.bioc.cmapR    

CMap Tools in R

Bioconductor version: Release (3.11)

The Connectivity Map (CMap) is a massive resource of perturbational gene expression profiles built by researchers at the Broad Institute and funded by the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) program. Please visit https://clue.io for more information. The cmapR package implements methods to parse, manipulate, and write common (CMap) data objects, such as annotated matrices and collections of gene sets.

Author: Ted Natoli [aut, cre]

Maintainer: Ted Natoli <ted.e.natoli at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cmapR")

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("cmapR")

 

HTML	R Script	cmapR Tutorial
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DataImport, DataRepresentation, GeneExpression, Software
Version	1.0.0
In Bioconductor since	BioC 3.11 (R-4.0) (0.5 years)
License	file LICENSE
Depends	R (>= 3.5)
Imports	methods, rhdf5, data.table, prada, SummarizedExperiment, matrixStats
LinkingTo
Suggests	knitr, testthat, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/cmap/cmapR
BugReports	https://github.com/cmap/cmapR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	cmapR_1.0.0.tar.gz
Windows Binary	cmapR_1.0.0.zip
macOS 10.13 (High Sierra)	cmapR_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/cmapR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/cmapR
Package Short Url	https://bioconductor.org/packages/cmapR/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive