README.md

Signac

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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://satijalab.org/signac/

Installation

Signac requires that Bioconductor is installed:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()
setRepositories(ind=1:2)

To install the latest release of Signac from CRAN:

install.packages("Signac")

To release the latest develop version from GitHub:

if (!requireNamespace("remotes", quietly = TRUE))
    install.packages("remotes")
remotes::install_github("timoast/signac", ref = "develop")

Release notes

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

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"
}

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Signac documentation built on March 18, 2022, 6:53 p.m.