Package: UPDhmm 1.3.0

Marta Sevilla

UPDhmm: Detecting Uniparental Disomy through NGS trio data

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).

Authors:Marta Sevilla [aut, cre], Carlos Ruiz-Arenas [aut]

UPDhmm_1.3.0.tar.gz
UPDhmm_1.3.0.zip(r-4.5)UPDhmm_1.3.0.zip(r-4.4)UPDhmm_1.3.0.zip(r-4.3)
UPDhmm_1.3.0.tgz(r-4.5-any)UPDhmm_1.3.0.tgz(r-4.4-any)UPDhmm_1.3.0.tgz(r-4.3-any)
UPDhmm_1.3.0.tar.gz(r-4.5-noble)UPDhmm_1.3.0.tar.gz(r-4.4-noble)
UPDhmm_1.3.0.tgz(r-4.4-emscripten)UPDhmm_1.3.0.tgz(r-4.3-emscripten)
UPDhmm.pdf |UPDhmm.html✨
UPDhmm/json (API)
NEWS

# Install 'UPDhmm' in R:
install.packages('UPDhmm', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/martasevilla/updhmm/issues

Datasets:
  • hmm - HMM data for predicting UPD events in trio genomic data

On BioConductor:UPDhmm-1.3.0(bioc 3.21)UPDhmm-1.2.0(bioc 3.20)

softwarehiddenmarkovmodelgenetics

4.54 score 1 stars 3 scripts 159 downloads 2 exports 71 dependencies

Last updated 4 months agofrom:025c593913. Checks:3 OK, 5 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 28 2025
R-4.5-winNOTEFeb 28 2025
R-4.5-macNOTEFeb 28 2025
R-4.5-linuxNOTEFeb 28 2025
R-4.4-winNOTEFeb 28 2025
R-4.4-macNOTEFeb 28 2025
R-4.3-winOKFeb 28 2025
R-4.3-macOKFeb 28 2025

Exports:calculateEventsvcfCheck

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesglueHMMhttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsVariantAnnotationvctrsXMLXVectoryaml

The UPDhmm's User Guide

Marta Sevilla Porras, Carlos Ruiz Arenas

Rendered fromUPDhmm.Rmdusingknitr::knitron Feb 28 2025.

Last update: 2024-04-25
Started: 2024-04-03