Package: UPDhmm
Title: Detecting Uniparental Disomy through NGS trio data
Version: 1.7.0
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,
  Biobase,
  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: 031c3fa
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
