Package Recipe 'bioconductor-podkat'

recipe bioconductor-podkat

Position-Dependent Kernel Association Test

Homepage: https://bioconductor.org/packages/3.14/bioc/html/podkat.html
License: GPL (>= 2)
Recipe: /bioconductor-podkat/meta.yaml
Links: biotools: podkat, doi: 10.1038/nmeth.3252

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.

package bioconductor-podkat¶

Versions

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

1.26.0-1, 1.26.0-0, 1.24.0-0, 1.22.0-1, 1.22.0-0, 1.20.0-0, 1.18.0-0, 1.16.0-1, 1.14.0-1, 1.14.0-0, 1.12.0-0, 1.10.0-0, 1.8.0-0

Depends

bioconductor-biobase >=2.54.0,<2.55.0
bioconductor-biocgenerics >=0.40.0,<0.41.0
bioconductor-biostrings >=2.62.0,<2.63.0
bioconductor-bsgenome >=1.62.0,<1.63.0
bioconductor-genomeinfodb >=1.30.0,<1.31.0
bioconductor-genomicranges >=1.46.0,<1.47.0
bioconductor-iranges >=2.28.0,<2.29.0
bioconductor-rhtslib >=1.26.0,<1.27.0
bioconductor-rsamtools >=2.10.0,<2.11.0
libblas >=3.8.0,<4.0a0
libgcc-ng >=10.3.0
liblapack >=3.8.0,<4.0a0
libstdcxx-ng >=10.3.0
r-base >=4.1,<4.2.0a0
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>)

Download stats¶

Link to this page¶

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