cmapR

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see cmapR.

CMap Tools in R


Bioconductor version: 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>

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

Installation

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

Details

biocViews DataImport, DataRepresentation, GeneExpression, Software
Version 1.0.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License file LICENSE
Depends R (>= 3.5)
Imports methods, rhdf5, data.table, prada, SummarizedExperiment, matrixStats
System Requirements
URL https://github.com/cmap/cmapR
Bug Reports https://github.com/cmap/cmapR/issues
See More
Suggests knitr, testthat, BiocStyle
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_1.0.0.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
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 3.11 Source Archive