hapFabia
hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
Bioconductor version: Release (3.17)
A package to identify very short IBD segments in large sequencing data by FABIA biclustering. Two haplotypes are identical by descent (IBD) if they share a segment that both inherited from a common ancestor. Current IBD methods reliably detect long IBD segments because many minor alleles in the segment are concordant between the two haplotypes. However, many cohort studies contain unrelated individuals which share only short IBD segments. This package provides software to identify short IBD segments in sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats.
Author: Sepp Hochreiter <hochreit at bioinf.jku.at>
Maintainer: Andreas Mitterecker <mitterecker at bioinf.jku.at>
citation("hapFabia")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("hapFabia")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("hapFabia")| hapFabia: Manual for the R package | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, GeneticVariability, Genetics, SNP, SequenceMatching, Sequencing, Software, Visualization |
| Version | 1.42.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (11 years) |
| License | LGPL (>= 2.1) |
| Depends | R (>= 3.6.0), Biobase, fabia(>= 2.3.1) |
| Imports | methods, graphics, grDevices, stats, utils |
| Linking To | |
| Suggests | |
| System Requirements | |
| Enhances | |
| URL | http://www.bioinf.jku.at/software/hapFabia/hapFabia.html |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | hapFabia_1.42.0.tar.gz |
| Windows Binary | hapFabia_1.42.0.zip (64-bit only) |
| macOS Binary (x86_64) | hapFabia_1.42.0.tgz |
| macOS Binary (arm64) | hapFabia_1.42.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/hapFabia |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/hapFabia |
| Bioc Package Browser | https://code.bioconductor.org/browse/hapFabia/ |
| Package Short Url | https://bioconductor.org/packages/hapFabia/ |
| Package Downloads Report | Download Stats |