recipe bioconductor-structuralvariantannotation

Variant annotations for structural variants

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/StructuralVariantAnnotation.html

License:

GPL-3 + file LICENSE

Recipe:

/bioconductor-structuralvariantannotation/meta.yaml

StructuralVariantAnnotation provides a framework for analysis of structural variants within the Bioconductor ecosystem. This package contains contains useful helper functions for dealing with structural variants in VCF format. The packages contains functions for parsing VCFs from a number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.

package bioconductor-structuralvariantannotation

Versions:

1.13.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1

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-iranges >=2.32.0,<2.33.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• bioconductor-variantannotation >=1.44.0,<1.45.0

• r-assertthat

• r-base >=4.2,<4.3.0a0

• r-dplyr

• r-rlang

• r-stringr

Required By:

• gridss

• bioconductor-svaretro

• bioconductor-svanumt

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-structuralvariantannotation

and update with:

conda update bioconductor-structuralvariantannotation

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-structuralvariantannotation:<tag>

(see bioconductor-structuralvariantannotation/tags for valid values for <tag>)

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