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This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.18 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see SCATEData.

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

Bioconductor version: Release (3.18)

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>

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


To install this package, start R (version "4.3") and enter:

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


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


Reference Manual PDF


biocViews ExperimentData, ExperimentHub, Genome, SNPData, SequencingData, SingleCellData, Software
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License MIT + file LICENSE
Depends parallel, preprocessCore, splines, splines2, xgboost, SCATEData, Rtsne, mclust
Imports utils, stats, GenomicAlignments, GenomicRanges
System Requirements
Bug Reports https://github.com/Winnie09/SCATE/issues
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Suggests rmarkdown, ggplot2, knitr
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Package Short Url https://bioconductor.org/packages/SCATE/
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