Package: Signac
Title: Analysis of Single-Cell Chromatin Data
Version: 1.17.1
Date: 2026-04-06
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: 7.3.3
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,
        pbapply, tidyr, patchwork, stats, utils, BiocGenerics, stringi,
        fastmatch, RcppRoll, scales, Rcpp, grid, tidyselect, vctrs,
        lifecycle, sparseMatrixStats, RSpectra
Collate: 'RcppExports.R' 'Signac-package.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'
        'ontology.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), SummarizedExperiment, TFBSTools, motifmatchr, BSgenome,
        shiny, miniUI, rtracklayer, biovizBase, Biostrings, lsa, MASS,
        wrswoR, fgsea
Roxygen: list(markdown = TRUE)
Config/pak/sysreqs: libbz2-dev libicu-dev liblzma-dev libssl-dev
        xz-utils zlib1g-dev
Repository: https://stuart-lab.r-universe.dev
Date/Publication: 2026-04-06 08:44:46 UTC
RemoteUrl: https://github.com/stuart-lab/signac
RemoteRef: HEAD
RemoteSha: 12d1ff82774890b08e55b3101f36fab83e674b88
NeedsCompilation: yes
Packaged: 2026-06-10 07:11:15 UTC; root
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>