recipe bioconductor-svanumt

NUMT detection from structural variant calls

Homepage:

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

License:

GPL-3 + file LICENSE

Recipe:

/bioconductor-svanumt/meta.yaml

svaNUMT contains functions for detecting NUMT events from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies NUMTs by nuclear-mitochondrial breakend junctions. The main function reports candidate NUMTs if there is a pair of valid insertion sites found on the nuclear genome within a certain distance threshold. The candidate NUMTs are reported by events.

package bioconductor-svanumt

versions:

1.8.0-0,  1.6.0-0,  1.4.0-0,  1.0.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-structuralvariantannotation:

>=1.18.0,<1.19.0

depends bioconductor-variantannotation:

>=1.48.0,<1.49.0

depends r-assertthat:

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

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-svanumt

and update with::

   mamba update bioconductor-svanumt

To create a new environment, run:

mamba create --name myenvname bioconductor-svanumt

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-svanumt:<tag>

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

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