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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>

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


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

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


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
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Suggests knitr, testthat (>= 2.1.0), BiocStyle, rmarkdown, markdown, karyoploteR, regioneR, dplyr
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Source Package UPDhmm_1.0.0.tar.gz
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