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) .

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 https://stuartlab.org/signac/

Installation

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

Release notes

For a changelog please see the NEWS file, also available on the Signac website.

Contributing

We welcome contributions to the Signac package. Please see the contribution guide for more information.

Getting help

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.

Citing Signac

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"
}