UPDhmm
This is the development version of UPDhmm; for the stable release version, see UPDhmm.
Detecting Uniparental Disomy through NGS trio data
Bioconductor version: Development (3.24)
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).
Author: Marta Sevilla [aut, cre] 
, Carlos Ruiz-Arenas [aut]
Maintainer: Marta Sevilla <marta.sevilla at upf.edu>
citation("UPDhmm")):Marta Sevilla, Carlos Ruiz-Arenas. UPDhmm: Detecting Uniparental Disomy through NGS trio data. doi:10.18129/B9.bioc.UPDhmm, R package version 1.9.0, https://bioconductor.org/packages/UPDhmm.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("UPDhmm")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("UPDhmm")| Long reads VCF Preprocessing User Guide | HTML | R Script |
| VCF Preprocessing User Guide | HTML | R Script |
| UPDhmm User Guide: From Detection to Postprocessing | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Genetics, HiddenMarkovModel, Software |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1.0) |
| Imports | HMM, utils, VariantAnnotation, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, stats, BiocParallel, GenomeInfoDb |
| System Requirements | |
| URL | https://github.com/martasevilla/UPDhmm |
| Bug Reports | https://github.com/martasevilla/UPDhmm/issues |
See More
| Suggests | knitr, testthat (>= 2.1.0), BiocStyle, rmarkdown, markdown, karyoploteR, regioneR, dplyr, BiocManager |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | UPDhmm_1.9.0.tar.gz |
| Windows Binary (x86_64) | UPDhmm_1.9.0.zip |
| macOS Binary (big-sur-x86_64) | UPDhmm_1.9.0.tgz |
| macOS Binary (sonoma-arm64) | UPDhmm_1.9.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/UPDhmm |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/UPDhmm |
| Package Short Url | https://bioconductor.org/packages/UPDhmm/ |
| Package Downloads Report | Download Stats |