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Signac Documentation

repository·master·Indexed 19 days ago

https://github.com/stuart-lab/signac

An R package for single-cell chromatin data analysis, including scATAC-seq, scCUT&Tag, scNTT-seq, and multimodal datasets. Signac provides tools for quality control, normalization, peak analysis, dimension reduction, clustering, and differential activity analysis, with seamless integration for Seurat and Bioconductor.

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What's inside Signac

  2. Overview of Signac features

    master

    Signac is an R package designed for the analysis of single-cell chromatin data, including scATAC-seq, scCUT&Tag, scNTT-seq, and multimodal datasets.

    Key capabilities include:

    • Peak Analysis: Calling peaks, identifying cell-type-specific peaks, and linking peaks to correlated genes.
    • Quantification & QC: Quantifying per-cell counts in genomic regions and calculating single-cell QC metrics.
    • Downstream Analysis: Dimensional reduction, visualization, clustering, sequence motif enrichment, and transcription factor footprinting.
    • Integration: Integrating multiple single-cell datasets and integrating with single-cell RNA-seq datasets.
    • Visualization: Visualizing 'pseudo-bulk' coverage tracks.
    • Ecosystem Compatibility: Seamless interface with Seurat, SeuratWrappers, and SeuratData; interoperability with Bioconductor tools; and parallelization via the future package.

  3. Install Signac from CRAN

    master

    To install the latest stable release of Signac from CRAN, use install.packages(). Note that setRepositories(ind=1:3) is required to ensure Bioconductor dependencies are automatically installed.

    setRepositories(ind=1:3) # needed to automatically install Bioconductor dependencies
install.packages("Signac")

  5. Install Signac development version from GitHub

    master

    To install the latest development version of Signac, use the remotes package to install directly from the stuart-lab/signac repository using the develop reference.

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

  6. Install Signac via R

    master

    You can install Signac from CRAN using the standard R installation commands. It is recommended to set the repositories to include CRAN, Bioconductor, and other relevant sources to ensure all dependencies are met.

    setRepositories(ind=1:3)
install.packages("Signac")