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CMap Tools in R

Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("cmapR")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

cmapR Tutorial HTML R Script
Reference Manual PDF


biocViews DataImport, DataRepresentation, GeneExpression, Software
Version 1.14.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License file LICENSE
Depends R (>= 4.0)
Imports methods, rhdf5, data.table, flowCore, SummarizedExperiment, matrixStats
System Requirements
URL https://github.com/cmap/cmapR
Bug Reports https://github.com/cmap/cmapR/issues
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Suggests knitr, testthat, BiocStyle, rmarkdown
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Package Archives

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

Source Package cmapR_1.14.0.tar.gz
Windows Binary cmapR_1.14.0.zip
macOS Binary (x86_64) cmapR_1.14.0.tgz
macOS Binary (arm64) cmapR_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cmapR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cmapR
Bioc Package Browser https://code.bioconductor.org/browse/cmapR/
Package Short Url https://bioconductor.org/packages/cmapR/
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