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This is the development version of scATAC.Explorer; for the stable release version, see scATAC.Explorer.

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

Bioconductor version: Development (3.20)

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))

# The following initializes usage of Bioc devel


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 1.11.0
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_1.11.0.tar.gz
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Source Repository (Developer Access) git clone
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