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A Collection of Single-cell ATAC Sequencing Datasets and Corresponding Metadata

Bioconductor version: Release (3.19)

This package provides a tool to search and download a collection of publicly available single cell ATAC-seq datasets and their metadata. scATAC-Explorer aims to act as a single point of entry for users looking to study single cell ATAC-seq data. Users can quickly search available datasets using the metadata table and download datasets of interest for immediate analysis within R.

Author: Arrian Gibson-Khademi [aut, cre], Erik Christensen [aut], Parisa Shooshtari [aut]

Maintainer: Arrian Gibson-Khademi <agibsonk at>

Citation (from within R, enter citation("scATAC.Explorer")):


To install this package, start R (version "4.4") and enter:

if (!require("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:

scATAC.Explorer HTML R Script
Reference Manual PDF


biocViews ExperimentData, ExpressionData, GEO, Genome, PackageTypeData, SequencingData, SingleCellData, Tissue
Version 1.10.0
License Artistic-2.0
Depends R (>= 4.1), SingleCellExperiment, BiocFileCache, data.table, utils, S4Vectors
Imports methods, Matrix
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Suggests BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package scATAC.Explorer_1.10.0.tar.gz
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Source Repository (Developer Access) git clone
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