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.

Version: 5.0.3
Depends: R (≥ 4.0.0), methods, SeuratObject (≥ 5.0.0)
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, leiden (≥ 0.3.1), lifecycle, lmtest, MASS, Matrix (≥ 1.5-0), matrixStats, miniUI, patchwork, pbapply, plotly (≥ 4.9.0), png, progressr, purrr, 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, BPCells, 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, presto, DelayedArray, harmony
Published: 2024-03-18
Author: Andrew Butler ORCID iD [ctb], Saket Choudhary 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], 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: 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.pdf

Downloads:

Package source: Seurat_5.0.3.tar.gz
Windows binaries: r-devel: Seurat_5.0.3.zip, r-release: Seurat_5.0.3.zip, r-oldrel: Seurat_5.0.3.zip
macOS binaries: r-release (arm64): Seurat_5.0.3.tgz, r-oldrel (arm64): Seurat_5.0.3.tgz, r-release (x86_64): Seurat_5.0.3.tgz
Old sources: Seurat archive

Reverse dependencies:

Reverse depends: CACIMAR, CelliD, phemd, ReactomeGSA.data, scAnnotatR, SCArray.sat, scCustomize, SCdeconR
Reverse imports: AnanseSeurat, APackOfTheClones, APL, bbknnR, benchdamic, CAMML, CDI, COTAN, CuratedAtlasQueryR, decontX, Dino, DR.SC, DWLS, GeneNMF, ggsc, ggsector, infercnv, mixhvg, nebula, partCNV, pipeComp, Platypus, PRECAST, ProFAST, RegionalST, rPanglaoDB, scAnnotate, scaper, scBFA, scBubbletree, scCB2, sccca, scDataviz, scDiffCom, scFeatures, scfetch, scGate, scGOclust, scMappR, scperturbR, scpoisson, SCRIP, scRNAseqApp, scRNAstat, scTreeViz, SignacX, singleCellTK, SoupX, Spaniel, SPECK, speckle, SpotClean, stJoincount, STREAK, tidyseurat
Reverse suggests: ASURAT, BayesSpace, BisqueRNA, Canek, cellpypes, CIARA, ClustAssess, clustifyr, clustifyrdatahub, clustree, combiroc, conos, consICA, countland, CRMetrics, CytoSimplex, DCATS, decoupleR, demuxSNP, DIscBIO, dittoSeq, dorothea, dyngen, EasyCellType, EpiMix, escape, escheR, FEAST, fgsea, GeomxTools, grandR, harmony, HCATonsilData, M3Drop, MOFA2, monocle, muscData, Nebulosa, nipalsMCIA, progeny, RESET, rliger, schex, SCORPIUS, SCpubr, scRepertoire, scTensor, Signac, SimBenchData, SimBu, SpatialDecon, spatialHeatmap, SPOTlight, TAPseq, TCGAbiolinks, tidybulk, treefit, tricycle, UCell, VAM
Reverse enhances: ReactomeGSA, SeuratObject

Linking:

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