recipe bioconductor-easylift

An R package to perform genomic liftover

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-easylift/meta.yaml

The easylift package provides a convenient tool for genomic liftover operations between different genome assemblies. It seamlessly works with Bioconductor's GRanges objects and chain files from the UCSC Genome Browser, allowing for straightforward handling of genomic ranges across various genome versions. One noteworthy feature of easylift is its integration with the BiocFileCache package. This integration automates the management and caching of chain files necessary for liftover operations. Users no longer need to manually specify chain file paths in their function calls, reducing the complexity of the liftover process.

package bioconductor-easylift

versions:

1.0.0-0

depends bioconductor-biocfilecache:

>=2.10.0,<2.11.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends r-base:

>=4.3,<4.4.0a0

depends r-r.utils:

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-easylift

and update with::

   mamba update bioconductor-easylift

To create a new environment, run:

mamba create --name myenvname bioconductor-easylift

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-easylift:<tag>

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

Download stats

Link to this page

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