recipe bioconductor-ucsc.utils

Low-level utilities to retrieve data from the UCSC Genome Browser

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/UCSC.utils.html

License:

Artistic-2.0

Recipe:

/bioconductor-ucsc.utils/meta.yaml

A set of low-level utilities to retrieve data from the UCSC Genome Browser. Most functions in the package access the data via the UCSC REST API but some of them query the UCSC MySQL server directly. Note that the primary purpose of the package is to support higher-level functionalities implemented in downstream packages like GenomeInfoDb or txdbmaker.

package bioconductor-ucsc.utils

(downloads) docker_bioconductor-ucsc.utils

versions:

1.2.0-0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends r-base:

>=4.4,<4.5.0a0

depends r-httr:

depends r-jsonlite:

requirements:

additional platforms:

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-ucsc.utils

and update with::

   mamba update bioconductor-ucsc.utils

To create a new environment, run:

mamba create --name myenvname bioconductor-ucsc.utils

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-ucsc.utils:<tag>

(see `bioconductor-ucsc.utils/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda 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-ucsc.utils/README.html)