Seurat: Tools for Single Cell Genomics

A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details.

Version: 2.3.1
Depends: R (≥ 3.4.0), ggplot2, cowplot, Matrix (≥ 1.2.14)
Imports: methods, ROCR, stringr, mixtools, lars, ica, tsne, Rtsne, fpc, ape, VGAM, pbapply, igraph, FNN, RANN, caret, dplyr, RColorBrewer, MASS, irlba, reshape2, gplots, gdata, Rcpp, tclust, ranger, dtw, SDMTools, plotly, diffusionMap, Hmisc, tidyr, ggridges, metap, lmtest, cluster, fitdistrplus, png, doSNOW, reticulate, foreach
LinkingTo: Rcpp, RcppEigen, RcppProgress
Suggests: testthat, loomR, S4Vectors, SummarizedExperiment, SingleCellExperiment, MAST, DESeq2
Published: 2018-05-05
Author: Rahul Satija [aut], Andrew Butler ORCID iD [aut], Paul Hoffman ORCID iD [aut, cre], Jeff Farrell [ctb], Shiwei Zheng ORCID iD [ctb], Christoph Hafemeister [ctb] (0000-0001-6365-8254), Patrick Roelli [ctb]
Maintainer: Paul Hoffman <seuratpackage at>
License: GPL-3 | file LICENSE
NeedsCompilation: yes
SystemRequirements: Java (>= 6)
Citation: Seurat citation info
Materials: README NEWS
CRAN checks: Seurat results


Reference manual: Seurat.pdf
Package source: Seurat_2.3.1.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
OS X binaries: r-release: Seurat_2.3.1.tgz, r-oldrel: Seurat_2.3.0.tgz
Old sources: Seurat archive

Reverse dependencies:

Reverse suggests: clustree


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