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: | 1.16.0 |
| 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,wrswoR |
| Published: | 2025-10-10 |
| DOI: | 10.32614/CRAN.package.Signac |
| Author: | Tim Stuart [aut, cre], Avi Srivastava [aut], Paul Hoffman [ctb], Rahul Satija [ctb] |
| Maintainer: | Tim Stuart <stuartt at a-star.edu.sg> |
| BugReports: | https://github.com/stuart-lab/signac/issues |
| License: | MIT + fileLICENSE |
| 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 |