recipe bioconductor-scatac.explorer

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






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.

package bioconductor-scatac.explorer

(downloads) docker_bioconductor-scatac.explorer



depends bioconductor-biocfilecache:


depends bioconductor-data-packages:


depends bioconductor-s4vectors:


depends bioconductor-singlecellexperiment:


depends curl:

depends r-base:


depends r-data.table:

depends r-matrix:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-scatac.explorer

and update with::

   mamba update bioconductor-scatac.explorer

To create a new environment, run:

mamba create --name myenvname bioconductor-scatac.explorer

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-scatac.explorer/tags`_ for valid values for ``<tag>``)

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