Position-Dependent Kernel Association Test

Bioconductor version: Release (3.19)

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.

Author: Ulrich Bodenhofer [aut,cre]

Maintainer: Ulrich Bodenhofer <ulrich at bodenhofer.com>

Citation (from within R, enter citation("podkat")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

PODKAT - An R Package for Association Testing Involving Rare and Private Variants PDF R Script
Reference Manual PDF


biocViews Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation, WholeGenome
Version 1.36.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License GPL (>= 2)
Depends R (>= 3.5.0), methods, Rsamtools(>= 1.99.1), GenomicRanges
Imports Rcpp (>= 0.11.1), parallel, stats (>= 4.3.0), graphics, grDevices, utils, Biobase, BiocGenerics, Matrix, GenomeInfoDb, IRanges, Biostrings, BSgenome(>= 1.32.0)
System Requirements GNU make
URL https://github.com/UBod/podkat
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Suggests BSgenome.Hsapiens.UCSC.hg38.masked, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools(>= 1.13.24), VariantAnnotation, SummarizedExperiment, knitr
Linking To Rcpp, Rhtslib(>= 1.15.3)
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Follow Installation instructions to use this package in your R session.

Source Package podkat_1.36.0.tar.gz
Windows Binary podkat_1.36.0.zip
macOS Binary (x86_64) podkat_1.36.0.tgz
macOS Binary (arm64) podkat_1.36.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/podkat
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/podkat
Bioc Package Browser https://code.bioconductor.org/browse/podkat/
Package Short Url https://bioconductor.org/packages/podkat/
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