UPDhmm
Detecting Uniparental Disomy through NGS trio data
Bioconductor version: Release (3.19)
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")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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")
Detection of UPDs in HTS data | HTML | R Script |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | Genetics, HiddenMarkovModel, Software |
Version | 1.0.0 |
In Bioconductor since | BioC 3.19 (R-4.4) (< 6 months) |
License | MIT + file LICENSE |
Depends | R (>= 4.3.0) |
Imports | HMM, utils, VariantAnnotation, GenomicRanges, S4Vectors, IRanges, stats |
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 |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | UPDhmm_1.0.0.tar.gz |
Windows Binary | UPDhmm_1.0.0.zip |
macOS Binary (x86_64) | UPDhmm_1.0.0.tgz |
macOS Binary (arm64) | UPDhmm_1.0.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/UPDhmm |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/UPDhmm |
Bioc Package Browser | https://code.bioconductor.org/browse/UPDhmm/ |
Package Short Url | https://bioconductor.org/packages/UPDhmm/ |
Package Downloads Report | Download Stats |