Package: UPDhmm 1.9.0
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:
UPDhmm_1.9.0.tar.gz
UPDhmm_1.9.0.zip(r-4.7)UPDhmm_1.9.0.zip(r-4.6)UPDhmm_1.9.0.zip(r-4.5)
UPDhmm_1.9.0.tgz(r-4.6-any)UPDhmm_1.9.0.tgz(r-4.5-any)
UPDhmm_1.9.0.tar.gz(r-4.7-any)UPDhmm_1.9.0.tar.gz(r-4.6-any)
UPDhmm_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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
- hmm - HMM data for predicting UPD events in trio genomic data
On BioConductor:UPDhmm-1.9.0(bioc 3.24)UPDhmm-1.8.0(bioc 3.23)
softwarehiddenmarkovmodelgenetics
Last updated from:deaeef8804. Checks:1 NOTE, 7 WARNING, 1 ERROR, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 177 | ||
| linux-devel-x86_64 | WARNING | 221 | ||
| source / vignettes | ERROR | 279 | ||
| linux-release-x86_64 | WARNING | 260 | ||
| macos-release-arm64 | WARNING | 104 | ||
| macos-oldrel-arm64 | WARNING | 145 | ||
| windows-devel | WARNING | 144 | ||
| windows-release | WARNING | 177 | ||
| windows-oldrel | WARNING | 131 | ||
| wasm-release | OK | 158 |
Exports:calculateEventscollapseEventsidentifyRecurrentRegionsmarkRecurrentRegionsvcfCheck
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesglueHMMhttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysUCSC.utilsVariantAnnotationvctrsXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate UPD events in trio VCFs. | calculateEvents |
| Collapse events per sample and chromosome | collapseEvents |
| HMM data for predicting UPD events in trio genomic data | hmm |
| Identify recurrent genomic regions across samples | identifyRecurrentRegions |
| Annotate regions as recurrent or non-recurrent | markRecurrentRegions |
| Check quality parameters (optional), change IDs and encode genotypes numerically | vcfCheck |