recipe bioconductor-hca

Exploring the Human Cell Atlas Data Coordinating Platform






This package provides users with the ability to query the Human Cell Atlas data repository for single-cell experiment data. The `projects()`, `files()`, `samples()` and `bundles()` functions retrieve summary information on each of these indexes; corresponding `*_details()` are available for individual entries of each index. File-based resources can be downloaded using `files_download()`. Advanced use of the package allows the user to page through large result sets, and to flexibly query the 'list-of-lists' structure representing query responses.

package bioconductor-hca

(downloads) docker_bioconductor-hca



depends bioconductor-biocfilecache:


depends r-base:


depends r-digest:

depends r-dplyr:

depends r-dt:

depends r-httr:

depends r-jsonlite:

depends r-miniui:

depends r-readr:

depends r-shiny:

depends r-tibble:

depends r-tidyr:



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-hca

and update with::

   mamba update bioconductor-hca

To create a new environment, run:

mamba create --name myenvname bioconductor-hca

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-hca/tags`_ for valid values for ``<tag>``)

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