DOI: 10.18129/B9.bioc.SCATE    

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

Bioconductor version: Release (3.12)

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>

Citation (from within R, enter citation("SCATE")):


To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


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


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



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


biocViews ExperimentData, ExperimentHub, Genome, SNPData, SequencingData, SingleCellData, Software
Version 1.0.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
License MIT + file LICENSE
Depends parallel, preprocessCore, splines, splines2, xgboost, SCATEData, Rtsne, mclust
Imports utils, stats, GenomicAlignments, GenomicRanges
Suggests rmarkdown, ggplot2, knitr
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_1.0.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) SCATE_1.0.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: