ZygosityPredictor

DOI: 10.18129/B9.bioc.ZygosityPredictor  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see ZygosityPredictor.

Package for prediction of zygosity for variants/genes in NGS data

Bioconductor version: 3.17

The ZygosityPredictor allows to predict how many copies of a gene are affected by small variants. In addition to the basic calculations of the affected copy number of a variant, the Zygosity-Predictor can integrate the influence of several variants on a gene and ultimately make a statement if and how many wild-type copies of the gene are left. This information proves to be of particular use in the context of translational medicine. For example, in cancer genomes, the Zygosity-Predictor can address whether unmutated copies of tumor-suppressor genes are present. Beyond this, it is possible to make this statement for all genes of an organism. The Zygosity-Predictor was primarily developed to handle SNVs and INDELs (later addressed as small-variants) of somatic and germline origin. In order not to overlook severe effects outside of the small-variant context, it has been extended with the assessment of large scale deletions, which cause losses of whole genes or parts of them.

Author: Marco Rheinnecker [aut, cre] , Marc Ruebsam [aut], Daniel Huebschmann [aut], Martina Froehlich [aut], Barbara Hutter [aut]

Maintainer: Marco Rheinnecker <marco.rheinnecker at dkfz-heidelberg.de>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ZygosityPredictor")

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("ZygosityPredictor")

 

HTML	R Script	ZygosityPredictor_Usage
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiomedicalInformatics, FunctionalPrediction, GenePrediction, Software, SomaticMutation
Version	1.0.3
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	GPL-2
Depends	R (>= 4.3.0)
Imports	GenomicAlignments, GenomicRanges, Rsamtools, IRanges, VariantAnnotation, DelayedArray, dplyr, stringr, purrr, tibble, methods, igraph
LinkingTo
Suggests	knitr, rmarkdown, testthat, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ZygosityPredictor_1.0.3.tar.gz
Windows Binary	ZygosityPredictor_1.0.3.zip
macOS Binary (x86_64)	ZygosityPredictor_1.0.3.tgz
macOS Binary (arm64)	ZygosityPredictor_1.0.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ZygosityPredictor
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ZygosityPredictor
Bioc Package Browser	https://code.bioconductor.org/browse/ZygosityPredictor/
Package Short Url	https://bioconductor.org/packages/ZygosityPredictor/
Package Downloads Report	Download Stats