UPDhmm

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see UPDhmm.

Detecting Uniparental Disomy through NGS trio data

Bioconductor version: 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

Need some help? Ask on the Bioconductor Support site!

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

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

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Package Archives

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

Source Package UPDhmm_1.0.0.tar.gz

Windows Binary (x86_64) 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/

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