Package: Signac
Title: Analysis of Single-Cell Chromatin Data
Version: 1.5.0
Date: 2021-12-07
Authors@R: c(
  person(given = 'Tim', family = 'Stuart', email = 'tstuart@nygenome.org', 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 (>= 4.0.0), methods
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.2
URL: https://github.com/timoast/signac, https://satijalab.org/signac
BugReports: https://github.com/timoast/signac/issues
LinkingTo: Rcpp
Imports: GenomeInfoDb, GenomicRanges, IRanges, Matrix, Rsamtools,
        S4Vectors, Seurat (>= 4.0.0), SeuratObject (>= 4.0.0),
        data.table, dplyr (>= 1.0.0), future, future.apply, ggplot2,
        ggseqlogo, irlba, pbapply, tidyr, patchwork, stats, utils,
        BiocGenerics, ggrepel, stringi, fastmatch, lsa, RcppRoll,
        scales, Rcpp, ggforce, qlcMatrix, grid
Collate: 'RcppExports.R' 'data.R' 'differential_accessibility.R'
        'generics.R' 'dimension_reduction.R' 'footprinting.R'
        'fragments.R' 'genomeinfodb-methods.R' 'granges-methods.R'
        'iranges-methods.R' 'links.R' 'mito.R' 'motifs.R' 'objects.R'
        'peaks.R' 'preprocessing.R' 'quantification.R' 'utilities.R'
        'visualization.R' 'zzz.R'
Suggests: testthat (>= 2.1.0), chromVAR, SummarizedExperiment,
        TFBSTools, motifmatchr, BSgenome, shiny, miniUI, rtracklayer,
        biovizBase, Biostrings
NeedsCompilation: yes
Packaged: 2021-12-07 17:23:14 UTC; stuartt
Author: Tim Stuart [aut, cre] (<https://orcid.org/0000-0002-3044-0897>),
  Avi Srivastava [aut] (<https://orcid.org/0000-0001-9798-2079>),
  Paul Hoffman [ctb] (<https://orcid.org/0000-0002-7693-8957>),
  Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>)
Maintainer: Tim Stuart <tstuart@nygenome.org>
Repository: CRAN
Date/Publication: 2021-12-08 17:40:06 UTC
Built: R 4.1.1; x86_64-apple-darwin13.4.0; 2021-12-08 20:37:06 UTC; unix
