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
git_url: https://git.bioconductor.org/packages/UPDhmm
git_branch: devel
git_last_commit: deaeef8
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.24
Date/Publication: 2026-06-01
NeedsCompilation: no
Packaged: 2026-06-01 22:10:09 UTC; biocbuild
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>
Built: R 4.6.0; ; 2026-06-02 04:18:49 UTC; unix
