DESCRIPTION

Package: Signac
Title: Analysis of Single-Cell Chromatin Data
Version: 1.14.0
Date: 2024-08-21
Authors@R: c(
  person(given = 'Tim', family = 'Stuart', email = 'stuartt@gis.a-star.edu.sg', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-3044-0897')),
  person(given = 'Avi', family = 'Srivastava', email = 'asrivastava@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0001-9798-2079')),
  person(given = 'Paul', family = 'Hoffman', email = 'phoffman@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0002-7693-8957')),
  person(given = 'Rahul', family = 'Satija', email = 'rsatija@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0001-9448-8833'))
  )
Description: A framework for the analysis and exploration of single-cell chromatin data.
    The 'Signac' package contains functions for quantifying single-cell chromatin data,
    computing per-cell quality control metrics, dimension reduction
    and normalization, visualization, and DNA sequence motif analysis.
    Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.
Depends:
    R (>= 4.1.0),
    methods
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
URL: https://github.com/stuart-lab/signac, https://stuartlab.org/signac
BugReports: https://github.com/stuart-lab/signac/issues
LinkingTo: Rcpp
Imports: 
    GenomeInfoDb (>= 1.29.3),
    GenomicRanges,
    IRanges,
    Matrix,
    Rsamtools,
    S4Vectors,
    SeuratObject (>= 5.0.2),
    data.table,
    dplyr (>= 1.0.0),
    future,
    future.apply,
    ggplot2,
    rlang,
    irlba,
    pbapply,
    tidyr,
    patchwork,
    stats,
    utils,
    BiocGenerics,
    stringi,
    fastmatch,
    RcppRoll,
    scales,
    Rcpp,
    grid,
    tidyselect,
    vctrs,
    lifecycle
Collate: 
    'RcppExports.R'
    'data.R'
    'differential_accessibility.R'
    'generics.R'
    'dimension_reduction.R'
    'footprinting.R'
    'fragments.R'
    'genomeinfodb-methods.R'
    'granges-methods.R'
    'heatmaps.R'
    'iranges-methods.R'
    'links.R'
    'mito.R'
    'motifs.R'
    'objects.R'
    'peaks.R'
    'preprocessing.R'
    'quantification.R'
    'region-enrichment.R'
    'utilities.R'
    'visualization.R'
    'zzz.R'
Suggests: 
    Seurat (>= 5.0.2),
    ggforce,
    ggrepel,
    ggseqlogo,
    testthat (>= 2.1.0),
    chromVAR,
    SummarizedExperiment,
    TFBSTools,
    motifmatchr,
    BSgenome,
    shiny,
    miniUI,
    rtracklayer,
    biovizBase,
    Biostrings,
    lsa,
    MASS