Package: Seurat
Version: 5.1.0
Date: 2024-05-08
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) <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.
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")
  )
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,
    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
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'
    'zzz.R'
    'integration5.R'
    'mixscape.R'
    'objects.R'
    'preprocessing.R'
    'preprocessing5.R'
    'roxygen.R'
    'sketching.R'
    'tree.R'
    'utilities.R'
RoxygenNote: 7.3.1
Encoding: UTF-8
Suggests:
    ape,
    arrow,
    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