podkat
Position-Dependent Kernel Association Test
Bioconductor version: Release (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 [aut,cre]
Maintainer: Ulrich Bodenhofer <ulrich at bodenhofer.com>
citation("podkat")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | R Script | |
Reference Manual | ||
NEWS | Text |
Details
biocViews | Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation, WholeGenome |
Version | 1.36.0 |
In Bioconductor since | BioC 3.1 (R-3.2) (9.5 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) |
System Requirements | GNU make |
URL | https://github.com/UBod/podkat |
See More
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 | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | podkat_1.36.0.tar.gz |
Windows Binary | podkat_1.36.0.zip |
macOS Binary (x86_64) | podkat_1.36.0.tgz |
macOS Binary (arm64) | podkat_1.36.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/podkat |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/podkat |
Bioc Package Browser | https://code.bioconductor.org/browse/podkat/ |
Package Short Url | https://bioconductor.org/packages/podkat/ |
Package Downloads Report | Download Stats |