UPDhmm

Detecting Uniparental Disomy through NGS trio data


Bioconductor version: Release (3.19)

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

Details

biocViews Genetics, HiddenMarkovModel, Software
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
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
See More
Suggests knitr, testthat (>= 2.1.0), BiocStyle, rmarkdown, markdown, karyoploteR, regioneR, dplyr
Linking To
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 UPDhmm_1.0.0.tar.gz
Windows Binary UPDhmm_1.0.0.zip
macOS Binary (x86_64) UPDhmm_1.0.0.tgz
macOS Binary (arm64) UPDhmm_1.0.0.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