Tools for Single Cell Genomics [R package Seurat version 5.3.1]

Rahul Satija

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.201505002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019年05月03日1>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.

Version: 5.3.1

Depends: R (≥ 4.0.0), methods, SeuratObject (≥ 5.0.2)

Imports: cluster, cowplot, fastDummies, fitdistrplus, future, future.apply, generics (≥ 0.1.3), ggplot2 (≥ 3.3.0), ggrepel, ggridges, graphics, grDevices, grid, httr, ica, igraph, irlba, jsonlite, KernSmooth, leidenbase, lifecycle, 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), RcppHNSW, reticulate, rlang, ROCR, RSpectra, Rtsne, scales, scattermore (≥ 1.2), sctransform (≥ 0.4.1), shiny, spatstat.explore, spatstat.geom, stats, tibble, tools, utils, uwot (≥ 0.1.10)

LinkingTo: Rcpp (≥ 0.11.0), RcppEigen, RcppProgress

Suggests: ape, arrow, Biobase, BiocGenerics, BPCells, data.table, DESeq2, DelayedArray, enrichR, GenomicRanges, GenomeInfoDb, glmGamPoi, ggrastr, harmony, hdf5r, IRanges, limma, MAST, metap, mixtools, monocle, presto, rsvd, R.utils, Rfast2, rtracklayer, S4Vectors, sf (≥ 1.0.0), SingleCellExperiment, SummarizedExperiment, testthat, VGAM

Published: 2025年10月29日

DOI: 10.32614/CRAN.package.Seurat

Author: Andrew Butler ORCID iD [ctb], Saket Choudhary ORCID iD [ctb], David Collins ORCID iD [ctb], Charlotte Darby ORCID iD [ctb], Jeff Farrell [ctb], Isabella Grabski ORCID iD [ctb], Christoph Hafemeister ORCID iD [ctb], Yuhan Hao ORCID iD [ctb], Austin Hartman ORCID iD [ctb], Paul Hoffman ORCID iD [ctb], Jaison Jain ORCID iD [ctb], Longda Jiang ORCID iD [ctb], Madeline Kowalski ORCID iD [ctb], Skylar Li [ctb], Gesmira Molla ORCID iD [ctb], Efthymia Papalexi ORCID iD [ctb], Patrick Roelli [ctb], Rahul Satija ORCID iD [aut, cre], Karthik Shekhar [ctb], Anagha Shenoy ORCID iD [ctb], Avi Srivastava ORCID iD [ctb], Tim Stuart ORCID iD [ctb], Kristof Torkenczy ORCID iD [ctb], Brian Zhang [ctb], Shiwei Zheng ORCID iD [ctb], Satija Lab and Collaborators [fnd]

Maintainer: Rahul Satija <seurat at nygenome.org>

BugReports: https://github.com/satijalab/seurat/issues

License: MIT + file LICENSE

URL: https://satijalab.org/seurat, https://github.com/satijalab/seurat

NeedsCompilation: yes

Additional_repositories: https://satijalab.r-universe.dev, https://bnprks.r-universe.dev

Citation: Seurat citation info

Materials: README, NEWS

In views: Omics

CRAN checks: Seurat results

Documentation:

Reference manual: Seurat.html , Seurat.pdf

Downloads:

Package source: Seurat_5.3.1.tar.gz

Windows binaries: r-devel: Seurat_5.3.1.zip, r-release: Seurat_5.3.1.zip, r-oldrel: Seurat_5.3.1.zip

macOS binaries: r-release (arm64): Seurat_5.3.1.tgz, r-oldrel (arm64): Seurat_5.3.1.tgz, r-release (x86_64): Seurat_5.3.1.tgz, r-oldrel (x86_64): Seurat_5.3.1.tgz

Old sources: Seurat archive

Reverse dependencies:

Reverse depends: CACIMAR, CelliD, ReactomeGSA.data, scAnnotatR, SCArray.sat, scCustomize, SCdeconR

Reverse imports: AnanseSeurat, APackOfTheClones, bbknnR, blase, CAESAR.Suite, CAMML, CatsCradle, CDI, ClustAssess, ClusterFoldSimilarity, COTAN, CSOA, CuratedAtlasQueryR, decontX, Dino, DOtools, DR.SC, DWLS, GeneNMF, ggsc, ggsector, HetSeq, infercnv, mixhvg, MOSim, nebula, partCNV, pipeComp, Platypus, PopComm, PoweREST, PRECAST, ProFAST, RegionalST, RepeatedHighDim, rPanglaoDB, scAnnotate, scaper, scBFA, scBubbletree, scCB2, sccca, sccore, scDataviz, scDiffCom, scDotPlot, scGate, scGOclust, scMappR, scperturbR, scPipeline, scpoisson, scRNAseqApp, scRNAstat, scStability, scTreeViz, SeuratExplorer, SignacX, SingleCellComplexHeatMap, singleCellTK, SlideCNA, SlimR, SoupX, SpaCCI, Spaniel, SPECK, speckle, SpotClean, stJoincount, stPipe, STREAK, tidyseurat, XYomics

Reverse suggests: anglemania, anndataR, ASURAT, Banksy, BayesSpace, Canek, cellpypes, CIARA, ClusterGVis, clustifyrdatahub, clustree, combiroc, conos, consICA, countland, CRMetrics, CytoSimplex, DamageDetective, DCATS, decoupleR, demuxSNP, DIscBIO, dittoSeq, dominoSignal, dorothea, dyngen, easybio, EasyCellType, EpiMix, escape, escheR, FEAST, fgsea, GeomxTools, grandR, harmony, HCATonsilData, HVP, immundata, jazzPanda, looking4clusters, M3Drop, mLLMCelltype, MOFA2, monocle, muscData, mxfda, myTAI, Nebulosa, nipalsMCIA, progeny, ReactomeGSA, RESET, rliger, rSWeeP, scGraphVerse, schex, scLANE, SCORPIUS, SCpubr, scRepertoire, scTensor, SETA, Signac, SimBenchData, SimBu, SpaNorm, SpatialDecon, SpatialFeatureExperiment, SuperCell, SuperCellCyto, TAPseq, TCGAbiolinks, tidybulk, treefit, tricycle, UCell, VAM, visiumStitched

Linking:

Please use the canonical form https://CRAN.R-project.org/package=Seurat to link to this page.