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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

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

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
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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