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
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
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