podkat

DOI: 10.18129/B9.bioc.podkat    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see podkat.

Position-Dependent Kernel Association Test

Bioconductor version: 3.13

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

Maintainer: Ulrich Bodenhofer <bodenhofer at bioinf.jku.at>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("podkat")

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

Documentation

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

browseVignettes("podkat")

 

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

Details

biocViews	Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation, WholeGenome
Version	1.24.0
In Bioconductor since	BioC 3.1 (R-3.2) (6.5 years)
License	GPL (>= 2)
Depends	R (>= 3.5.0), methods, Rsamtools(>= 1.99.1), GenomicRanges
Imports	Rcpp (>= 0.11.1), parallel, stats, graphics, grDevices, utils, Biobase, BiocGenerics, Matrix, GenomeInfoDb, IRanges, Biostrings, BSgenome(>= 1.32.0)
LinkingTo	Rcpp, Rhtslib(>= 1.15.3)
Suggests	BSgenome.Hsapiens.UCSC.hg38.masked, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools(>= 1.13.24), VariantAnnotation, SummarizedExperiment, knitr
SystemRequirements	GNU make
Enhances
URL	http://www.bioinf.jku.at/software/podkat/ https://github.com/UBod/podkat
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	podkat_1.24.0.tar.gz
Windows Binary	podkat_1.24.0.zip
macOS 10.13 (High Sierra)	podkat_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/podkat
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/podkat
Package Short Url	https://bioconductor.org/packages/podkat/
Package Downloads Report	Download Stats