Package: Seurat Version: 5.2.1 Title: Tools for Single Cell Genomics Description: 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) , Macosko E, Basu A, Satija R, et al (2015) , Stuart T, Butler A, et al (2019) , and Hao, Hao, et al (2020) for more details. Authors@R: c( person(given = "Andrew", family = "Butler", email = "abutler@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0003-3608-0463")), person(given = "Saket", family = "Choudhary", email = "schoudhary@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-5202-7633")), person(given = 'David', family = 'Collins', email = 'dcollins@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0001-9243-7821')), person(given = "Charlotte", family = "Darby", email = "cdarby@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0003-2195-5300")), person(given = "Jeff", family = "Farrell", email = "jfarrell@g.harvard.edu", role = "ctb"), person(given = "Isabella", family = "Grabski", email = "igrabski@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-0616-5469")), person(given = "Christoph", family = "Hafemeister", email = "chafemeister@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-6365-8254")), person(given = "Yuhan", family = "Hao", email = "yhao@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-1810-0822")), person(given = "Austin", family = "Hartman", email = "ahartman@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-7278-1852")), person(given = "Paul", family = "Hoffman", email = "hoff0792@umn.edu", role = "ctb", comment = c(ORCID = "0000-0002-7693-8957")), person(given = "Jaison", family = "Jain", email = "jjain@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-9478-5018")), person(given = "Longda", family = "Jiang", email = "ljiang@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0003-4964-6497")), person(given = "Madeline", family = "Kowalski", email = "mkowalski@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-5655-7620")), person(given = "Skylar", family = "Li", email = "sli@nygenome.org", role = "ctb"), person(given = "Gesmira", family = "Molla", email = 'gmolla@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0002-8628-5056')), person(given = "Efthymia", family = "Papalexi", email = "epapalexi@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-5898-694X")), person(given = "Patrick", family = "Roelli", email = "proelli@nygenome.org", role = "ctb"), person(given = "Rahul", family = "Satija", email = "seurat@nygenome.org", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9448-8833")), person(given = "Karthik", family = "Shekhar", email = "kshekhar@berkeley.edu", role = "ctb"), person(given = "Avi", family = "Srivastava", email = "asrivastava@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-9798-2079")), person(given = "Tim", family = "Stuart", email = "tstuart@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-3044-0897")), person(given = "Kristof", family = "Torkenczy", email = "", role = "ctb", comment = c(ORCID = "0000-0002-4869-7957")), person(given = "Shiwei", family = "Zheng", email = "szheng@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-6682-6743")), person("Satija Lab and Collaborators", role = "fnd") ) License: MIT + file LICENSE URL: https://satijalab.org/seurat, https://github.com/satijalab/seurat BugReports: https://github.com/satijalab/seurat/issues Additional_repositories: https://satijalab.r-universe.dev, https://bnprks.r-universe.dev 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) 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 LinkingTo: Rcpp (>= 0.11.0), RcppEigen, RcppProgress BuildManual: true Encoding: UTF-8 LazyData: true RoxygenNote: 7.3.2 Collate: 'RcppExports.R' 'reexports.R' 'generics.R' 'clustering.R' 'visualization.R' 'convenience.R' 'data.R' 'differential_expression.R' 'dimensional_reduction.R' 'integration.R' 'zzz.R' 'integration5.R' 'mixscape.R' 'objects.R' 'preprocessing.R' 'preprocessing5.R' 'roxygen.R' 'sketching.R' 'tree.R' 'utilities.R' Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev Repository: https://mojaveazure.r-universe.dev Date/Publication: 2025-01-24 17:49:18 UTC RemoteUrl: https://github.com/satijalab/seurat RemoteRef: develop RemoteSha: 5c0a2665e26e6e0b1b2527a823b526d15d76d5a3 NeedsCompilation: yes Packaged: 2026-06-08 23:00:59 UTC; root Author: Andrew Butler [ctb] (ORCID: ), Saket Choudhary [ctb] (ORCID: ), David Collins [ctb] (ORCID: ), Charlotte Darby [ctb] (ORCID: ), Jeff Farrell [ctb], Isabella Grabski [ctb] (ORCID: ), Christoph Hafemeister [ctb] (ORCID: ), Yuhan Hao [ctb] (ORCID: ), Austin Hartman [ctb] (ORCID: ), Paul Hoffman [ctb] (ORCID: ), Jaison Jain [ctb] (ORCID: ), Longda Jiang [ctb] (ORCID: ), Madeline Kowalski [ctb] (ORCID: ), Skylar Li [ctb], Gesmira Molla [ctb] (ORCID: ), Efthymia Papalexi [ctb] (ORCID: ), Patrick Roelli [ctb], Rahul Satija [aut, cre] (ORCID: ), Karthik Shekhar [ctb], Avi Srivastava [ctb] (ORCID: ), Tim Stuart [ctb] (ORCID: ), Kristof Torkenczy [ctb] (ORCID: ), Shiwei Zheng [ctb] (ORCID: ), Satija Lab and Collaborators [fnd] Maintainer: Rahul Satija