Package: Signac
Title: Analysis of Single-Cell Chromatin Data
Version: 1.15.0
Date: 2025-08-17
Authors@R: c(
  person(given = 'Tim', family = 'Stuart', email = 'stuartt@a-star.edu.sg', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-3044-0897')),
  person(given = 'Avi', family = 'Srivastava', email = 'asrivastava@wistar.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
NeedsCompilation: yes
Packaged: 2025-08-18 14:58:02 UTC; tim
Author: Tim Stuart [aut, cre] (ORCID: <https://orcid.org/0000-0002-3044-0897>),
  Avi Srivastava [aut] (ORCID: <https://orcid.org/0000-0001-9798-2079>),
  Paul Hoffman [ctb] (ORCID: <https://orcid.org/0000-0002-7693-8957>),
  Rahul Satija [ctb] (ORCID: <https://orcid.org/0000-0001-9448-8833>)
Maintainer: Tim Stuart <stuartt@a-star.edu.sg>
Repository: CRAN
Date/Publication: 2025-08-18 19:00:25 UTC
Built: R 4.5.1; x86_64-w64-mingw32; 2025-10-06 03:07:23 UTC; windows
Archs: x64
