recipe bioconductor-podkat

This package provides an association test that is capable of dealing with very rare and even private variants. This is accomplished by a kernel-based approach that takes the positions of the variants into account. The test can be used for pre-processed matrix data, but also directly for variant data stored in VCF files. Association testing can be performed whole-genome, whole-exome, or restricted to pre-defined regions of interest. The test is complemented by tools for analyzing and visualizing the results.

Homepage

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

License

GPL (>= 2)

Recipe

/bioconductor-podkat/meta.yaml

Links

biotools: podkat, doi: 10.1038/nmeth.3252

package bioconductor-podkat

Versions

1.14.0-1, 1.14.0-0, 1.12.0-0, 1.10.0-0, 1.8.0-0

Depends

• bioconductor-biobase >=2.42.0,<2.43.0

• bioconductor-biocgenerics >=0.28.0,<0.29.0

• bioconductor-biostrings >=2.50.0,<2.51.0

• bioconductor-bsgenome >=1.50.0,<1.51.0

• bioconductor-genomeinfodb >=1.18.0,<1.19.0

• bioconductor-genomicranges >=1.34.0,<1.35.0

• bioconductor-iranges >=2.16.0,<2.17.0

• bioconductor-rsamtools >=1.34.0,<1.35.0

• libgcc-ng >=7.3.0

• libstdcxx-ng >=7.3.0

• r-base >=3.5.1,<3.5.2.0a0

• r-matrix

• r-rcpp >=0.11.1

Required By

Installation

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

conda install bioconductor-podkat

and update with:

conda update bioconductor-podkat

or use the docker container:

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

(see bioconductor-podkat/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-podkat/README.html)