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: |
1.9.0 |
| Depends: |
R (≥ 4.0.0), methods |
| Imports: |
GenomeInfoDb (≥ 1.29.3), GenomicRanges, IRanges, Matrix, Rsamtools, S4Vectors, SeuratObject (≥ 4.0.0), data.table, dplyr (≥ 1.0.0), future, future.apply, ggplot2, irlba, pbapply, tidyr, patchwork, stats, utils, BiocGenerics, stringi, fastmatch, RcppRoll, scales, Rcpp, grid, tidyselect, vctrs |
| LinkingTo: |
Rcpp |
| Suggests: |
Seurat (≥ 4.0.6), ggforce, ggrepel, ggseqlogo, testthat (≥
2.1.0), chromVAR, SummarizedExperiment, TFBSTools, motifmatchr, BSgenome, shiny, miniUI, rtracklayer, biovizBase, Biostrings, lsa, qlcMatrix |
| Published: |
2022-12-08 |
| Author: |
Tim Stuart  [aut,
cre],
Avi Srivastava
[aut],
Paul Hoffman
[ctb],
Rahul Satija
[ctb] |
| Maintainer: |
Tim Stuart <tstuart at nygenome.org> |
| 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 |
| CRAN checks: |
Signac results |