recipe bioconductor-variantfiltering

Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/VariantFiltering.html

License

Artistic-2.0

Recipe

/bioconductor-variantfiltering/meta.yaml

Links

biotools: variantfiltering, doi: 10.1038/nmeth.3252

package bioconductor-variantfiltering

(downloads) docker_bioconductor-variantfiltering

Versions

1.18.0-0, 1.16.0-0, 1.14.0-0

Depends bioconductor-annotationdbi

>=1.44.0,<1.45.0

Depends bioconductor-biobase

>=2.42.0,<2.43.0

Depends bioconductor-biocgenerics

>=0.28.0,<0.29.0

Depends bioconductor-biocparallel

>=1.16.0,<1.17.0

Depends bioconductor-biostrings

>=2.50.0,<2.51.0

Depends bioconductor-bsgenome

>=1.50.0,<1.51.0

Depends bioconductor-genomeinfodb

>=1.18.0,<1.19.0

Depends bioconductor-genomicfeatures

>=1.34.0,<1.35.0

Depends bioconductor-genomicranges

>=1.34.0,<1.35.0

Depends bioconductor-genomicscores

>=1.6.0,<1.7.0

Depends bioconductor-graph

>=1.60.0,<1.61.0

Depends bioconductor-gviz

>=1.26.0,<1.27.0

Depends bioconductor-iranges

>=2.16.0,<2.17.0

Depends bioconductor-rbgl

>=1.58.0,<1.59.0

Depends bioconductor-rsamtools

>=1.34.0,<1.35.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends bioconductor-summarizedexperiment

>=1.12.0,<1.13.0

Depends bioconductor-variantannotation

>=1.28.0,<1.29.0

Depends bioconductor-xvector

>=0.22.0,<0.23.0

Depends libgcc-ng

>=7.3.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-dt

Depends r-shiny

Depends r-shinyjs

Depends r-shinythemes

Depends r-shinytree

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-variantfiltering

and update with:

conda update bioconductor-variantfiltering

or use the docker container:

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

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