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: 2.3.4
Depends: R (≥ 3.4.0), ggplot2, cowplot, Matrix (≥ 1.2.14)
Imports: methods, ROCR, mixtools, lars, ica, tsne, Rtsne, fpc, ape, pbapply, igraph, RANN, dplyr, RColorBrewer, MASS, irlba, reshape2, gplots, Rcpp (≥ 0.11.0), dtw, SDMTools, plotly, Hmisc, httr, tidyr, ggridges, metap, lmtest, cluster, fitdistrplus, png, doSNOW, reticulate, foreach, hdf5r
LinkingTo: Rcpp (≥ 0.11.0), RcppEigen, RcppProgress
Suggests: gdata, VGAM, tclust, testthat, caret, ranger, loomR, phateR, S4Vectors, made4, SummarizedExperiment, SingleCellExperiment, MAST, DESeq2, destiny
Published: 2018-07-17
Author: Rahul Satija ORCID iD [aut], Andrew Butler ORCID iD [aut], Paul Hoffman ORCID iD [aut, cre], Jeff Farrell [ctb], Shiwei Zheng ORCID iD [ctb], Christoph Hafemeister ORCID iD [ctb], Patrick Roelli [ctb]
Maintainer: Paul Hoffman <seuratpackage at gmail.com>
BugReports: https://github.com/satijalab/seurat/issues
License: GPL-3 | file LICENSE
URL: http://www.satijalab.org/seurat, https://github.com/satijalab/seurat
NeedsCompilation: yes
Citation: Seurat citation info
Materials: README NEWS
CRAN checks: Seurat results

Downloads:

Reference manual: Seurat.pdf
Package source: Seurat_2.3.4.tar.gz
Windows binaries: r-devel: Seurat_2.3.3.zip, r-release: Seurat_2.3.3.zip, r-oldrel: Seurat_2.3.2.zip
OS X binaries: r-release: Seurat_2.3.3.tgz, r-oldrel: Seurat_2.3.3.tgz
Old sources: Seurat archive

Reverse dependencies:

Reverse suggests: clustree

Linking:

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