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

Detecting Uniparental Disomy through NGS trio data

Bioconductor version: Development (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>

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


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

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

# The following initializes usage of Bioc devel


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 1.1.0
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_1.1.0.tar.gz
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