Package: Seurat Version: 4.4.0 Date: 2023-09-26 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 = "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 = "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 = "seurat@nygenome.org", role = c("aut", "cre"), 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 = "Madeline", family = "Kowalski", email = "mkowalski@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-5655-7620")), 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 = "rsatija@nygenome.org", role = "ctb", 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") ) URL: https://satijalab.org/seurat, https://github.com/satijalab/seurat BugReports: https://github.com/satijalab/seurat/issues 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, purrr, RANN, RColorBrewer, Rcpp (>= 1.0.7), RcppAnnoy (>= 0.0.18), reticulate, rlang, ROCR, Rtsne, SeuratObject (>= 4.1.4), scales, scattermore (>= 1.2), sctransform (>= 0.4.0), shiny, spatstat.explore, spatstat.geom, stats, tibble, tools, utils, uwot (>= 0.1.14) LinkingTo: Rcpp (>= 0.11.0), RcppEigen, RcppProgress License: MIT + file LICENSE LazyData: true Collate: 'RcppExports.R' 'reexports.R' 'generics.R' 'clustering.R' 'visualization.R' 'convenience.R' 'data.R' 'differential_expression.R' 'dimensional_reduction.R' 'integration.R' 'mixscape.R' 'objects.R' 'preprocessing.R' 'tree.R' 'utilities.R' 'zzz.R' RoxygenNote: 7.2.3 Encoding: UTF-8 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 Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev Repository: https://satijalab.r-universe.dev Date/Publication: 2024-01-10 16:15:10 UTC RemoteUrl: https://github.com/satijalab/seurat RemoteRef: seurat4 RemoteSha: 74905f1be2f14438e55b8cd3c96e89e6d13b4857 NeedsCompilation: yes Packaged: 2026-06-24 11:01:59 UTC; root Author: Andrew Butler [ctb] (ORCID: ), Saket Choudhary [ctb] (ORCID: ), Charlotte Darby [ctb] (ORCID: ), Jeff Farrell [ctb], Christoph Hafemeister [ctb] (ORCID: ), Yuhan Hao [ctb] (ORCID: ), Austin Hartman [ctb] (ORCID: ), Paul Hoffman [aut, cre] (ORCID: ), Jaison Jain [ctb] (ORCID: ), Madeline Kowalski [ctb] (ORCID: ), Efthymia Papalexi [ctb] (ORCID: ), Patrick Roelli [ctb], Rahul Satija [ctb] (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: Paul Hoffman