clusterExperiment

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see clusterExperiment.

Compare Clusterings for Single-Cell Sequencing

Bioconductor version: 3.12

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 "4.0") 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 2.10.1

In Bioconductor since BioC 3.4 (R-3.3) (7.5 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, howmany, locfdr, matrixStats, graphics, parallel, RSpectra, 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

Linking To Rcpp

Enhances

Depends On Me netSmooth

Imports Me netDx

Suggests Me slingshot, tradeSeq

Links To Me

Build Report Build Report