podkat
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see podkat.
Position-Dependent Kernel Association Test
Bioconductor version: 3.9
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("podkat")):
Installation
To install this package, start R (version "3.6") 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 | 1.16.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.2.0), methods, Rsamtools(>= 1.99.1), GenomicRanges |
| Imports | Rcpp (>= 0.11.1), parallel, stats, graphics, grDevices, utils, Biobase, BiocGenerics, Matrix, GenomeInfoDb, IRanges, Biostrings, BSgenome(>= 1.32.0) |
| System Requirements | |
| URL | http://www.bioinf.jku.at/software/podkat/ 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_1.16.0.tar.gz |
| Windows Binary | podkat_1.16.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | podkat_1.16.0.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 |
| Old Source Packages for BioC 3.9 | Source Archive |