recipe bioconductor-snapcount

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

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/snapcount.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-snapcount/meta.yaml

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

versions:

1.14.0-0,  1.12.0-0,  1.10.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.2.0-0,  1.0.0-0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-assertthat:

depends r-base:

>=4.3,<4.4.0a0

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:

requirements:

Installation

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 quay.io/biocontainers/bioconductor-snapcount:<tag>

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

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-snapcount/README.html)