clusterExperiment

This is the released version of clusterExperiment; for the devel version, see clusterExperiment.

Compare Clusterings for Single-Cell Sequencing

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DOI: 10.18129/B9.bioc.clusterExperiment

Bioconductor version: Release (3.22)

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]

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

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

Installation

To install this package, start R (version "4.5") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("clusterExperiment")

clusterExperiment Vignette HTML R Script

Working with Large Datasets HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Clustering, RNASeq, Sequencing, SingleCell, Software

Version 2.30.0

In Bioconductor since BioC 3.4 (R-3.3) (9 years)

License Artistic-2.0

Depends R (>= 3.6.0), SingleCellExperiment, SummarizedExperiment(>= 1.15.4), BiocGenerics

Imports methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats, limma, locfdr, matrixStats, graphics, parallel, BiocSingular, kernlab, stringr, S4Vectors, grDevices, DelayedArray(>= 0.7.48), HDF5Array(>= 1.7.10), Matrix, Rcpp, edgeR, scales, zinbwave, phylobase, pracma, mbkmeans

System Requirements

URL

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

Suggests BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph, rmarkdown

Linking To Rcpp

Enhances

Depends On Me netSmooth

Imports Me

Suggests Me slingshot, tradeSeq

Links To Me

Build Report Build Report

Package Archives

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

Source Package clusterExperiment_2.30.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) clusterExperiment_2.30.0.tgz

macOS Binary (arm64) clusterExperiment_2.30.0.tgz

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

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

Bioc Package Browser https://code.bioconductor.org/browse/clusterExperiment/

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

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