recipe bioconductor-variantfiltering

Filtering of coding and non-coding genetic variants

Homepage

https://bioconductor.org/packages/3.12/bioc/html/VariantFiltering.html

License

Artistic-2.0

Recipe

/bioconductor-variantfiltering/meta.yaml

Links

biotools: variantfiltering, doi: 10.1038/nmeth.3252

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.

package bioconductor-variantfiltering

Versions

1.26.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0

Depends

• bioconductor-annotationdbi >=1.52.0,<1.53.0

• bioconductor-biobase >=2.50.0,<2.51.0

• bioconductor-biocgenerics >=0.36.0,<0.37.0

• bioconductor-biocparallel >=1.24.0,<1.25.0

• bioconductor-biostrings >=2.58.0,<2.59.0

• bioconductor-bsgenome >=1.58.0,<1.59.0

• bioconductor-genomeinfodb >=1.26.0,<1.27.0

• bioconductor-genomicfeatures >=1.42.0,<1.43.0

• bioconductor-genomicranges >=1.42.0,<1.43.0

• bioconductor-genomicscores >=2.2.0,<2.3.0

• bioconductor-graph >=1.68.0,<1.69.0

• bioconductor-gviz >=1.34.0,<1.35.0

• bioconductor-iranges >=2.24.0,<2.25.0

• bioconductor-rbgl >=1.66.0,<1.67.0

• bioconductor-rsamtools >=2.6.0,<2.7.0

• bioconductor-s4vectors >=0.28.0,<0.29.0

• bioconductor-summarizedexperiment >=1.20.0,<1.21.0

• bioconductor-variantannotation >=1.36.0,<1.37.0

• bioconductor-xvector >=0.30.0,<0.31.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=7.5.0

• liblapack >=3.8.0,<4.0a0

• r-base >=4.0,<4.1.0a0

• r-dt

• r-shiny

• r-shinyjs

• r-shinythemes

• r-shinytree

Required By

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>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-variantfiltering/README.html)