https://github.com/stuart-lab/signac
R toolkit for the analysis of single-cell chromatin data
https://github.com/stuart-lab/signac
atac bioinformatics single-cell
Last synced: 4 months ago
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R toolkit for the analysis of single-cell chromatin data
- Host: GitHub
- URL: https://github.com/stuart-lab/signac
- Owner: stuart-lab
- License: other
- Created: 2019-05-09T22:32:26.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2026-01-20T08:57:03.000Z (5 months ago)
- Last Synced: 2026-01-31T09:52:43.308Z (4 months ago)
- Topics: atac, bioinformatics, single-cell
- Language: R
- Homepage: https://stuartlab.org/signac/
- Size: 13.7 MB
- Stars: 403
- Watchers: 4
- Forks: 100
- Open Issues: 19
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: .github/CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
# Signac 
[](https://github.com/stuart-lab/signac/actions)
[](https://cran.r-project.org/package=Signac)
[](https://cran.r-project.org/package=Signac)
## Overview
Signac is a comprehensive R package for the analysis of single-cell
chromatin data. Signac includes functions for quality control,
normalization, dimension reduction, clustering, differential activity,
and more.
Documentation and tutorials can be found at
## Installation
To install the latest release of Signac from CRAN:
``` r
setRepositories(ind=1:3) # needed to automatically install Bioconductor dependencies
install.packages("Signac")
```
To release the latest develop version from GitHub:
``` r
if (!requireNamespace("remotes", quietly = TRUE))
install.packages("remotes")
remotes::install_github("stuart-lab/signac", ref = "develop")
```
## Release notes
For a changelog please see the [NEWS
file](https://github.com/stuart-lab/signac/blob/develop/NEWS.md), also
available on the [Signac
website](https://stuartlab.org/signac/news/index.html).
## Contributing
We welcome contributions to the Signac package. Please see the
[contribution guide](https://github.com/stuart-lab/signac/blob/develop/CONTRIBUTING.md)
for more information.
## Getting help
If you encounter a bug or have a feature request, please open an
[issue](https://github.com/stuart-lab/signac/issues).
If you would like to discuss questions related to single-cell analysis,
you can open a
[discussion](https://github.com/stuart-lab/signac/discussions).
## Citing Signac
If you use the Signac package in your work please cite [Stuart et
al. 2021](https://doi.org/10.1038/s41592-021-01282-5)
```
@ARTICLE{signac,
title = "Single-cell chromatin state analysis with Signac",
author = "Stuart, Tim and Srivastava, Avi and Madad, Shaista and Lareau,
Caleb A and Satija, Rahul",
journal = "Nat. Methods",
publisher = "Nature Publishing Group",
pages = "1--9",
month = nov,
year = 2021,
url = "https://www.nature.com/articles/s41592-021-01282-5",
language = "en"
}
```
## Related packages
- [Seurat](https://github.com/satijalab/seurat)
- [SeuratObject](https://github.com/satijalab/seurat-object)
- [SeuratDisk](https://github.com/mojaveazure/seurat-disk)
- [SeuratData](https://github.com/satijalab/seurat-data)
- [SeuratWrappers](https://github.com/satijalab/seurat-wrappers)
- [Azimuth](https://github.com/satijalab/azimuth)