recipe bioconductor-snapcount

R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts






snapcount is a client interface to the Snaptron webservices which support querying by gene name or genomic region. Results include raw expression counts derived from alignment of RNA-seq samples and/or various summarized measures of expression across one or more regions/genes per-sample (e.g. percent spliced in).

package bioconductor-snapcount

(downloads) docker_bioconductor-snapcount



depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-summarizedexperiment:


depends r-assertthat:

depends r-base:


depends r-data.table:

depends r-httr:

depends r-jsonlite:

depends r-magrittr:

depends r-matrix:

depends r-purrr:

depends r-r6:

depends r-rlang:

depends r-stringr:



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-snapcount

and update with::

   mamba update bioconductor-snapcount

To create a new environment, run:

mamba create --name myenvname bioconductor-snapcount

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

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