- recipe bioconductor-svanumt
NUMT detection from structural variant calls
- Homepage:
https://bioconductor.org/packages/3.16/bioc/html/svaNUMT.html
- License:
GPL-3 + file LICENSE
- Recipe:
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:
1.4.0-0
,1.0.0-0
- Depends:
bioconductor-biocgenerics
>=0.44.0,<0.45.0
bioconductor-biostrings
>=2.66.0,<2.67.0
bioconductor-genomeinfodb
>=1.34.0,<1.35.0
bioconductor-genomicfeatures
>=1.50.0,<1.51.0
bioconductor-genomicranges
>=1.50.0,<1.51.0
bioconductor-rtracklayer
>=1.58.0,<1.59.0
bioconductor-s4vectors
>=0.36.0,<0.37.0
bioconductor-structuralvariantannotation
>=1.13.0,<1.14.0
bioconductor-variantannotation
>=1.44.0,<1.45.0
r-base
>=4.2,<4.3.0a0
- Required By:
Installation
With an activated Bioconda channel (see set-up-channels), install with:
conda install bioconductor-svanumt
and update with:
conda update bioconductor-svanumt
or 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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Link to this page¶
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