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) , Macosko E, Basu A, Satija R, et al (2015) , and Butler A and Satija R (2017) for more details.


Reference manual

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2.1.0 by Paul Hoffman, a month ago,

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Browse source code at

Authors: Rahul Satija [aut], Andrew Butler [aut], Paul Hoffman [aut, cre], Jeff Farrell [ctb], Shiwei Zheng [ctb], Christoph Hafemeister [ctb], Patrick Roelli [ctb]

Documentation:   PDF Manual  

GPL-3 | file LICENSE license

Imports methods, ROCR, stringr, mixtools, lars, ica, tsne, Rtsne, fpc, ape, VGAM, pbapply, igraph, FNN, caret, dplyr, RColorBrewer, MASS, irlba, reshape2, gridExtra, gplots, gdata, Rcpp, tclust, ranger, NMF, dtw, SDMTools, plotly, diffusionMap, Hmisc, tidyr, ggjoy

Depends on ggplot2, cowplot, Matrix

Suggests testthat, SummarizedExperiment, MAST, DESeq2

Linking to Rcpp, RcppEigen, RcppProgress

System requirements: Java (>= 1.6)

See at CRAN