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Bioconductor - podkat (development version)

podkat

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

Position-Dependent Kernel Association Test

Bioconductor version: Development (3.22)

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")): Installation

To install this package, start R (version "4.5") 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 1.41.0 In Bioconductor since BioC 3.1 (R-3.2) (10 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 See More Package Archives

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

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