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podkat

This is the development version of podkat; for the stable release version, see podkat.

Position-Dependent Kernel Association Test


Bioconductor version: Development (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

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

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation, WholeGenome
Version 1.35.0
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 http://www.bioinf.jku.at/software/podkat/ https://github.com/UBod/podkat
See More
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)
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package podkat_1.35.0.tar.gz
Windows Binary podkat_1.35.0.zip
macOS Binary (x86_64) podkat_1.35.0.tgz
macOS Binary (arm64) podkat_1.35.0.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/
Package Downloads Report Download Stats