cmapR

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see cmapR.

CMap Tools in R

Bioconductor version: 3.14

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")):

Installation

To install this package, start R (version "4.1") and enter:


if (!require("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")

cmapR Tutorial HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, DataRepresentation, GeneExpression, Software

Version 1.6.0

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

Suggests knitr, testthat, BiocStyle, rmarkdown

Linking To

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Build Report Build Report

Package Archives

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

Source Package cmapR_1.6.0.tar.gz

Windows Binary cmapR_1.6.0.zip

macOS 10.13 (High Sierra) cmapR_1.6.0.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/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.14 Source Archive