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hapFabia

This is the development version of hapFabia; for the stable release version, see hapFabia.

hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data


Bioconductor version: Development (3.19)

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 (from within R, enter citation("hapFabia")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, GeneticVariability, Genetics, SNP, SequenceMatching, Sequencing, Software, Visualization
Version 1.45.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License LGPL (>= 2.1)
Depends R (>= 3.6.0), Biobase, fabia(>= 2.3.1)
Imports methods, graphics, grDevices, stats, utils
System Requirements
URL http://www.bioinf.jku.at/software/hapFabia/hapFabia.html
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package hapFabia_1.45.0.tar.gz
Windows Binary hapFabia_1.45.0.zip
macOS Binary (x86_64) hapFabia_1.45.0.tgz
macOS Binary (arm64) hapFabia_1.45.0.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/
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