podkat
Position-Dependent Kernel Association Test
Bioconductor version: 3.23 · Package version: 1.44.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("podkat")Details
| Maintainer | Ulrich Bodenhofer <ulrich@bodenhofer.com> |
| Author | Ulrich Bodenhofer [aut, cre] |
| License | GPL (>= 2) |
| URL | https://github.com/UBod/podkat |
| System Requirements | GNU make |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation, WholeGenome |
| Package Short Url | https://bioconductor.org/packages/podkat/ |
Citation
From within R, enter citation("podkat"):
Ulrich Bodenhofer. podkat: Position-Dependent Kernel Association Test. doi:10.18129/B9.bioc.podkat, R package version 1.44.0, https://bioconductor.org/packages/podkat.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | podkat_1.44.0.tar.gz |
| Windows binary (x86_64) | podkat_1.44.0.zip |
| macOS binary (arm64) | podkat_1.44.0.tgz |
| macOS binary (x86_64) | podkat_1.44.0.tgz |
Dependencies
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, Seqinfo, 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