Package: podkat
Type: Package
Title: Position-Dependent Kernel Association Test
Version: 1.34.0
Date: 2022-11-16
Author: Ulrich Bodenhofer
Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Description: 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.
URL: http://www.bioinf.jku.at/software/podkat/
        https://github.com/UBod/podkat
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)
Suggests: BSgenome.Hsapiens.UCSC.hg38.masked,
        TxDb.Hsapiens.UCSC.hg38.knownGene,
        BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools (>= 1.13.24),
        VariantAnnotation, SummarizedExperiment, knitr
LinkingTo: Rcpp, Rhtslib (>= 1.15.3)
SystemRequirements: GNU make
VignetteBuilder: knitr
Collate: AllGenerics.R AllClasses.R inputChecks.R sort-methods.R
        show-methods.R print-methods.R summary-methods.R
        p.adjust-methods.R c-methods.R access-methods.R
        coerce-methods.R resampling.R unmaskedRegions.R
        partitionRegions-methods.R genotypeMatrix-methods.R
        computeKernel.R computePvalues.R readGenotypeMatrix-methods.R
        readVariantInfo-methods.R readSampleNamesFromVcfHeader.R
        readRegionsFromBedFile.R weightFuncs.R assocTest-methods.R
        nullModel-methods.R qqplot-methods.R plot-methods.R
        filterResult-methods.R split-methods.R computeWeights.R
        weights-methods.R
biocViews: Genetics, WholeGenome, Annotation, VariantAnnotation,
        Sequencing, DataImport
NeedsCompilation: yes
git_url: https://git.bioconductor.org/packages/podkat
git_branch: RELEASE_3_18
git_last_commit: 0a4ab12
git_last_commit_date: 2023-10-24
Date/Publication: 2023-10-24
Packaged: 2023-10-24 22:13:27 UTC; biocbuild
Built: R 4.3.1; x86_64-apple-darwin20; 2023-10-25 05:00:20 UTC; unix
