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>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.

Depends: R (≥ 4.0.0), 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 (≥ 1.5-0), matrixStats, miniUI, patchwork, pbapply, plotly (≥ 4.9.0), png, progressr, RANN, RColorBrewer, Rcpp (≥ 1.0.7), RcppAnnoy (≥ 0.0.18), reticulate, rlang, ROCR, Rtsne, scales, scattermore (≥ 0.7), sctransform (≥ 0.3.5), SeuratObject (≥ 4.1.3), shiny, spatstat.explore, spatstat.geom, stats, tibble, tools, utils, uwot (≥ 0.1.14)
LinkingTo: Rcpp (≥ 0.11.0), RcppEigen, RcppProgress
Suggests: ape, rsvd, testthat, hdf5r, S4Vectors, SummarizedExperiment, SingleCellExperiment, MAST, DESeq2, BiocGenerics, GenomicRanges, GenomeInfoDb, IRanges, rtracklayer, Rfast2, monocle, Biobase, VGAM, limma, metap, enrichR, mixtools, ggrastr, data.table, R.utils
Published: 2023-06-22
Author: Andrew Butler ORCID iD [ctb], Saket Choudhary ORCID iD [ctb], Charlotte Darby ORCID iD [ctb], Jeff Farrell [ctb], Christoph Hafemeister ORCID iD [ctb], Yuhan Hao ORCID iD [ctb], Austin Hartman ORCID iD [ctb], Paul Hoffman ORCID iD [aut, cre], Jaison Jain ORCID iD [ctb], Madeline Kowalski ORCID iD [ctb], Efthymia Papalexi ORCID iD [ctb], Patrick Roelli [ctb], Rahul Satija ORCID iD [ctb], Karthik Shekhar [ctb], Avi Srivastava ORCID iD [ctb], Tim Stuart ORCID iD [ctb], Kristof Torkenczy ORCID iD [ctb], Shiwei Zheng ORCID iD [ctb], Satija Lab and Collaborators [fnd]
Maintainer: Paul Hoffman <seurat at>
License: MIT + file LICENSE
NeedsCompilation: yes
Citation: Seurat citation info
Materials: README NEWS
In views: Omics
CRAN checks: Seurat results


Reference manual: Seurat.pdf


Package source: Seurat_4.3.0.1.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): Seurat_4.3.0.1.tgz, r-oldrel (arm64): Seurat_4.3.0.1.tgz, r-release (x86_64): Seurat_4.3.0.1.tgz, r-oldrel (x86_64): Seurat_4.3.0.1.tgz
Old sources: Seurat archive

Reverse dependencies:

Reverse depends: CACIMAR, CelliD, phemd,, scAnnotatR, SCArray.sat, scCustomize, schex
Reverse imports: AnanseSeurat, APL, bbknnR, benchdamic, CAMML, CIDER, COTAN, CSCDRNA, Dino, DR.SC, DWLS, ggsector, gsdensity, infercnv, IRISFGM, mixhvg, Nebulosa, pipeComp, PRECAST, ProFAST, rPanglaoDB, scAnnotate, scBFA, scBubbletree, scCB2, scDataviz, scDiffCom, scFeatures, scGate, scMappR, scperturbR, scpoisson, SCRIP, scRNAseqApp, scRNAstat, scTreeViz, SignacX, singleCellTK, SoupX, Spaniel, SPECK, speckle, SpotClean, stJoincount, STREAK
Reverse suggests: ASURAT, BayesSpace, BisqueRNA, Canek, cellpypes, CIARA, ClustAssess, clustifyr, clustifyrdatahub, clustree, combiroc, conos, countland, CRMetrics, decoupleR, DIscBIO, dittoSeq, dorothea, dyngen, EasyCellType, EpiMix, escape, fcoex, FEAST, fgsea, GeomxTools, grandR, harmony, M3Drop, MOFA2, monocle, muscData, progeny, RESET, rliger, SCORPIUS, SCpubr, scRepertoire, scTensor, Signac, SimBenchData, SimBu, spatialHeatmap, SPOTlight, TAPseq, TCGAbiolinks, tidybulk, treefit, tricycle, UCell, VAM
Reverse enhances: ReactomeGSA


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