UPDhmm

This is the released version of UPDhmm; for the devel version, see UPDhmm.

Detecting Uniparental Disomy through NGS trio data

Bioconductor version: Release (3.20)

Uniparental disomy (UPD) is a genetic condition where an individual inherits both copies of a chromosome or part of it from one parent, rather than one copy from each parent. This package contains a HMM for detecting UPDs through HTS (High Throughput Sequencing) data from trio assays. By analyzing the genotypes in the trio, the model infers a hidden state (normal, father isodisomy, mother isodisomy, father heterodisomy and mother heterodisomy).

Author: Marta Sevilla [aut, cre] , Carlos Ruiz-Arenas [aut]

Maintainer: Marta Sevilla <marta.sevilla at upf.edu>

Citation (from within R, enter citation("UPDhmm")):

Installation

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


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

BiocManager::install("UPDhmm")

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("UPDhmm")

Detection of UPDs in HTS data	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Genetics, HiddenMarkovModel, Software
Version	1.2.0
In Bioconductor since	BioC 3.19 (R-4.4) (0.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.3.0)
Imports	HMM, utils, VariantAnnotation, GenomicRanges, S4Vectors, IRanges, stats
System Requirements
URL	https://github.com/martasevilla/UPDhmm
Bug Reports	https://github.com/martasevilla/UPDhmm/issues

Suggests	knitr, testthat (>= 2.1.0), BiocStyle, rmarkdown, markdown, karyoploteR, regioneR, dplyr
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Build Report	Build Report

Package Archives

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

Source Package	UPDhmm_1.2.0.tar.gz
Windows Binary (x86_64)	UPDhmm_1.2.0.zip
macOS Binary (x86_64)	UPDhmm_1.2.0.tgz
macOS Binary (arm64)	UPDhmm_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/UPDhmm
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/UPDhmm
Bioc Package Browser	https://code.bioconductor.org/browse/UPDhmm/
Package Short Url	https://bioconductor.org/packages/UPDhmm/
Package Downloads Report	Download Stats