To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("podkat")
In most cases, you don't need to download the package archive at all.
podkat
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Position-Dependent Kernel Association Test
Bioconductor version: Release (3.4)
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")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("podkat")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("podkat")
| R Script | PODKAT - An R Package for Association Testing Involving Rare and Private Variants | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation, WholeGenome |
| Version | 1.6.1 |
| In Bioconductor since | BioC 3.1 (R-3.2) (2 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.2.0), methods, Rsamtools, GenomicRanges |
| Imports | Rcpp (>= 0.11.1), parallel, stats, graphics, grDevices, utils, Biobase, BiocGenerics, Matrix, GenomeInfoDb, IRanges, Biostrings, BSgenome(>= 1.32.0) |
| LinkingTo | Rcpp, Rsamtools |
| Suggests | BSgenome.Hsapiens.UCSC.hg38.masked, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools(>= 1.13.24), VariantAnnotation, SummarizedExperiment, knitr |
| SystemRequirements | |
| Enhances | |
| URL | http://www.bioinf.jku.at/software/podkat/ |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | podkat_1.6.1.tar.gz |
| Windows Binary | podkat_1.6.1.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | podkat_1.6.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/podkat/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/podkat/ |
| Package Downloads Report | Download Stats |
Documentation »
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