Package: UPDhmm
Title: Detecting Uniparental Disomy through NGS trio data
Version: 1.9.0
BugReports: https://github.com/martasevilla/UPDhmm/issues
Authors@R: 
  c(person(given = "Marta",
     family = "Sevilla",
     role= c("aut", "cre"),
     email = "marta.sevilla@upf.edu",
     comment = c(ORCID = "0009-0005-0179-920X")),
     person(given = "Carlos",
     family = "Ruiz-Arenas",
     role= c("aut"),
     email = "cruizarenas@unav.es",
     comment = c(ORCID = "0000-0002-6014-3498")))
Description: 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).
biocViews: Software, HiddenMarkovModel, Genetics
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.3.3
Depends: R (>= 4.1.0)
Imports: HMM, utils, VariantAnnotation, GenomicRanges, S4Vectors,
        IRanges, SummarizedExperiment, stats, BiocParallel,
        GenomeInfoDb
Suggests: knitr, testthat (>= 2.1.0), BiocStyle, rmarkdown, markdown,
        karyoploteR, regioneR, dplyr, BiocManager
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
URL: https://github.com/martasevilla/UPDhmm
Language: en-US
Config/pak/sysreqs: make libbz2-dev liblzma-dev libpng-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:02:51 UTC
RemoteUrl: https://github.com/bioc/UPDhmm
RemoteRef: HEAD
RemoteSha: deaeef88048ef062aa33dc2e0d1e32a13adff863
NeedsCompilation: no
Packaged: 2026-07-02 07:27:34 UTC; root
Author: Marta Sevilla [aut, cre] (ORCID:
    <https://orcid.org/0009-0005-0179-920X>),
  Carlos Ruiz-Arenas [aut] (ORCID:
    <https://orcid.org/0000-0002-6014-3498>)
Maintainer: Marta Sevilla <marta.sevilla@upf.edu>