DOI: 10.18129/B9.bioc.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")):


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


biocViews Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation, WholeGenome
Version 1.35.0
In Bioconductor since BioC 3.1 (R-3.2) (8.5 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)
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
URL http://www.bioinf.jku.at/software/podkat/ https://github.com/UBod/podkat
Depends On Me
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Source Package podkat_1.35.0.tar.gz
Windows Binary podkat_1.35.0.zip
macOS Binary (x86_64) podkat_1.35.0.tgz
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Package Short Url https://bioconductor.org/packages/podkat/
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