recipe bioconductor-hpastainr

Queries the Human Protein Atlas Staining Data for Multiple Proteins and Genes






This package is built around the HPAStainR function. The purpose of the HPAStainR function is to query the visual staining data in the Human Protein Atlas to return a table of staining ranked cell types. The function also has multiple arguments to personalize to output as well to include cancer data, csv readable names, modify the confidence levels of the results and more. The other functions exist exclusively to easily acquire the data required to run HPAStainR.

package bioconductor-hpastainr

(downloads) docker_bioconductor-hpastainr



depends r-base:


depends r-data.table:

depends r-dplyr:

depends r-scales:

depends r-shiny:

depends r-stringr:

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-hpastainr

and update with::

   mamba update bioconductor-hpastainr

To create a new environment, run:

mamba create --name myenvname bioconductor-hpastainr

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

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