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Signac: Analysis of Single-Cell Chromatin Data

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>.

Version: 1.14.0
Depends: R (≥ 4.1.0), methods
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
LinkingTo: Rcpp
Suggests: Seurat (≥ 5.0.2), ggforce, ggrepel, ggseqlogo, testthat (≥ 2.1.0), chromVAR, SummarizedExperiment, TFBSTools, motifmatchr, BSgenome, shiny, miniUI, rtracklayer, biovizBase, Biostrings, lsa, MASS
Published: 2024-08-21
DOI: 10.32614/CRAN.package.Signac
Author: Tim Stuart ORCID iD [aut, cre], Avi Srivastava ORCID iD [aut], Paul Hoffman ORCID iD [ctb], Rahul Satija ORCID iD [ctb]
Maintainer: Tim Stuart <stuartt at gis.a-star.edu.sg>
BugReports: https://github.com/stuart-lab/signac/issues
License: MIT + file LICENSE
URL: https://github.com/stuart-lab/signac, https://stuartlab.org/signac
NeedsCompilation: yes
Citation: Signac citation info
Materials: README NEWS
In views: Omics
CRAN checks: Signac results

Documentation:

Reference manual: Signac.pdf

Downloads:

Package source: Signac_1.14.0.tar.gz
Windows binaries: r-devel: Signac_1.14.0.zip, r-release: Signac_1.14.0.zip, r-oldrel: Signac_1.14.0.zip
macOS binaries: r-release (arm64): Signac_1.14.0.tgz, r-oldrel (arm64): Signac_1.14.0.tgz, r-release (x86_64): Signac_1.14.0.tgz, r-oldrel (x86_64): Signac_1.14.0.tgz
Old sources: Signac archive

Reverse dependencies:

Reverse imports: MOSim
Reverse suggests: AnanseSeurat, ChromSCape, HCATonsilData

Linking:

Please use the canonical form https://CRAN.R-project.org/package=Signac to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.