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 https://stuartlab.org/signac/
To install the latest release of Signac from CRAN:
setRepositories(ind=1:3) # needed to automatically install Bioconductor dependencies
install.packages("Signac")To release the latest develop version from GitHub:
if (!requireNamespace("remotes", quietly = TRUE))
install.packages("remotes")
remotes::install_github("stuart-lab/signac", ref = "develop")To install the Signac v2 beta version:
if (!requireNamespace("remotes", quietly = TRUE))
install.packages("remotes")
remotes::install_github("stuart-lab/signac", ref = "v2")Documentation for the v2 beta can be found here
For a changelog please see the NEWS file, also available on the Signac website.
We welcome contributions to the Signac package. Please see the contribution guide for more information.
If you encounter a bug or have a feature request, please open an issue.
If you would like to discuss questions related to single-cell analysis, you can open a discussion.
If you use the Signac package in your work please cite Stuart et al. 2021
@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"
}