- 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¶
- 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:
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
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-scatac.explorer:<tag> (see `bioconductor-scatac.explorer/tags`_ for valid values for ``<tag>``)