UPDhmm
This is the released version of UPDhmm; for the devel version, see UPDhmm.
Detecting Uniparental Disomy through NGS trio data
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| Long reads VCF Preprocessing User Guide | HTML | R Script |
| UPDhmm User Guide: From Detection to Postprocessing | HTML | R Script |
| VCF Preprocessing User Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Genetics, HiddenMarkovModel, Software |
| Version | 1.8.0 |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | UPDhmm_1.8.0.tar.gz |
| Windows Binary (x86_64) | UPDhmm_1.8.0.zip |
| macOS Binary (big-sur-x86_64) | UPDhmm_1.8.0.tgz |
| macOS Binary (sonoma-arm64) | UPDhmm_1.8.0.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 |