podkat
This is the development version of podkat; for the stable release version, see podkat.
Position-Dependent Kernel Association Test
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.45.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11.5 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, Seqinfo, 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_1.45.0.tar.gz |
| Windows Binary (x86_64) | podkat_1.45.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | podkat_1.45.0.tgz |
| macOS Binary (sonoma-arm64) | podkat_1.45.0.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 |