SCATE

DOI: 10.18129/B9.bioc.SCATE  

SCATE: Single-cell ATAC-seq Signal Extraction and Enhancement

Bioconductor version: Release (3.16)

SCATE is a software tool for extracting and enhancing the sparse and discrete Single-cell ATAC-seq Signal. Single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) is the state-of-the-art technology for analyzing genome-wide regulatory landscapes in single cells. Single-cell ATAC-seq data are sparse and noisy, and analyzing such data is challenging. Existing computational methods cannot accurately reconstruct activities of individual cis-regulatory elements (CREs) in individual cells or rare cell subpopulations. SCATE was developed to adaptively integrate information from co-activated CREs, similar cells, and publicly available regulome data and substantially increase the accuracy for estimating activities of individual CREs. We demonstrate that SCATE can be used to better reconstruct the regulatory landscape of a heterogeneous sample.

Author: Zhicheng Ji [aut], Weiqiang Zhou [aut], Wenpin Hou [cre, aut] , Hongkai Ji [aut]

Maintainer: Wenpin Hou <wp.hou3 at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SCATE")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SCATE")

 

HTML	R Script	1. SCATE package
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ExperimentData, ExperimentHub, Genome, SNPData, SequencingData, SingleCellData, Software
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	MIT + file LICENSE
Depends	parallel, preprocessCore, splines, splines2, xgboost, SCATEData, Rtsne, mclust
Imports	utils, stats, GenomicAlignments, GenomicRanges
LinkingTo
Suggests	rmarkdown, ggplot2, knitr
SystemRequirements
Enhances
URL
BugReports	https://github.com/Winnie09/SCATE/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SCATE_1.8.0.tar.gz
Windows Binary	SCATE_1.8.0.zip (64-bit only)
macOS Binary (x86_64)	SCATE_1.8.0.tgz
macOS Binary (arm64)	SCATE_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SCATE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SCATE
Bioc Package Browser	https://code.bioconductor.org/browse/SCATE/
Package Short Url	https://bioconductor.org/packages/SCATE/
Package Downloads Report	Download Stats