clusterExperiment
This is the development version of clusterExperiment; for the stable release version, see clusterExperiment.
Compare Clusterings for Single-Cell Sequencing
Bioconductor version: Development (3.21)
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("clusterExperiment")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | 2.27.0 |
| 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 | 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_2.27.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |