clusterExperiment

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see clusterExperiment.

Compare Clusterings for Single-Cell Sequencing

Bioconductor version: 3.6

Provides functionality for running and comparing many different clusterings of single-cell sequencing data or other large mRNA Expression data sets.

Author: Elizabeth Purdom [aut, cre, cph], Davide Risso [aut], Marla Johnson [ctb]

Maintainer: Elizabeth Purdom <epurdom at stat.berkeley.edu>

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

Installation

To install this package, start R (version "3.4") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("clusterExperiment")

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

Documentation

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Clustering, RNASeq, Sequencing, SingleCell, Software

Version 1.4.0

In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)

License Artistic-2.0

Depends R (>= 3.4), SummarizedExperiment

Imports methods, NMF, RColorBrewer, ape, phylobase, cluster, stats, limma, dendextend, howmany, locfdr, matrixStats, graphics, parallel, RSpectra, kernlab, stringr

System Requirements

URL

Bug Reports https://github.com/epurdom/clusterExperiment/issues

Suggests BiocStyle, knitr, testthat, scRNAseq, MAST

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 clusterExperiment_1.4.0.tar.gz

Windows Binary clusterExperiment_1.4.0.zip

Mac OS X 10.11 (El Capitan) clusterExperiment_1.4.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/clusterExperiment

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/clusterExperiment

Package Short Url https://bioconductor.org/packages/clusterExperiment/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.6 Source Archive