cmapR

DOI: 10.18129/B9.bioc.cmapR    

This is the development version of cmapR; for the stable release version, see cmapR.

CMap Tools in R

Bioconductor version: Development (3.12)

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.0
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
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_1.1.0.tar.gz
Windows Binary cmapR_1.1.0.zip
macOS 10.13 (High Sierra) cmapR_1.1.0.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

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