clusterExperiment
Compare Clusterings for Single-Cell Sequencing
Bioconductor version: Release (3.19)
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 "4.4") 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
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 | ||
NEWS | Text |
Details
biocViews | Clustering, RNASeq, Sequencing, SingleCell, Software |
Version | 2.24.0 |
In Bioconductor since | BioC 3.4 (R-3.3) (8 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 |
See More
Suggests | BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph, rmarkdown |
Linking To | Rcpp |
Enhances | |
Depends On Me | netSmooth |
Imports Me | |
Suggests Me | netDx, 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_2.24.0.tar.gz |
Windows Binary | clusterExperiment_2.24.0.zip |
macOS Binary (x86_64) | clusterExperiment_2.24.0.tgz |
macOS Binary (arm64) | clusterExperiment_2.24.0.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/ |
Package Downloads Report | Download Stats |