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 Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more details.

Version: 3.2.2
Depends: R (≥ 3.6.0), methods
Imports: cluster, cowplot, fitdistrplus, future, future.apply, ggplot2 (≥ 3.3.0), ggrepel, ggridges, graphics, grDevices, grid, httr, ica, igraph, irlba, jsonlite, KernSmooth, leiden (≥ 0.3.1), lmtest, MASS, Matrix (≥ 1.2-14), matrixStats, miniUI, patchwork, pbapply, plotly (≥ 4.9.0), png, RANN, RColorBrewer, Rcpp, RcppAnnoy, reticulate, rlang, ROCR, rsvd, Rtsne, scales, sctransform (≥ 0.3.0), shiny, spatstat, stats, tibble, tools, utils, uwot (≥ 0.1.5)
LinkingTo: Rcpp (≥ 0.11.0), RcppEigen, RcppProgress
Suggests: loomR, ape, testthat, hdf5r, S4Vectors, SummarizedExperiment, SingleCellExperiment, MAST, DESeq2, BiocGenerics, GenomicRanges, GenomeInfoDb, IRanges, rtracklayer, Rfast2, monocle, Biobase, VGAM, limma, metap
Published: 2020-09-26
Author: Rahul Satija ORCID iD [aut], Andrew Butler ORCID iD [aut], Paul Hoffman ORCID iD [aut, cre], Tim Stuart ORCID iD [aut], Jeff Farrell [ctb], Shiwei Zheng ORCID iD [ctb], Christoph Hafemeister ORCID iD [ctb], Patrick Roelli [ctb], Yuhan Hao ORCID iD [ctb]
Maintainer: Paul Hoffman <nygcSatijalab at>
License: GPL-3 | file LICENSE
NeedsCompilation: yes
Citation: Seurat citation info
Materials: README NEWS
CRAN checks: Seurat results


Reference manual: Seurat.pdf
Package source: Seurat_3.2.2.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release: Seurat_3.2.2.tgz, r-oldrel: Seurat_3.2.2.tgz
Old sources: Seurat archive

Reverse dependencies:

Reverse depends:, scAlign, schex, Spaniel, tidyseurat
Reverse imports: celda, Nebulosa, phemd, pipeComp, scBFA, scCB2, scDataviz, scMAGeCK, scMappR, scRepertoire, Signac, singleCellTK, SoupX
Reverse suggests: BayesSpace, BisqueRNA, clustifyrdatahub, clustree, DIscBIO, dittoSeq, dorothea, escape, fcoex, M3Drop, MOFA2, monocle, muscData, nanny, progeny, Rmagic, scSorter, scTensor, singleCellHaystack, TAPseq, tidybulk, treefit, zinbwave
Reverse enhances: ReactomeGSA


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