ZygosityPredictor

This is the development version of ZygosityPredictor; for the stable release version, see ZygosityPredictor.

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

Bioconductor version: Development (3.21)

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] (ORCID: ), Marc Ruebsam [aut], Daniel Huebschmann [aut], Martina Froehlich [aut], Barbara Hutter [aut]

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

Citation (from within R, enter citation("ZygosityPredictor")):

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

Usage	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiomedicalInformatics, FunctionalPrediction, GenePrediction, Software, SomaticMutation
Version	1.7.0
In Bioconductor since	BioC 3.17 (R-4.3) (1.5 years)
License	GPL-2
Depends	R (>= 4.3.0)
Imports	GenomicAlignments, GenomicRanges, Rsamtools, IRanges, VariantAnnotation, DelayedArray, dplyr, stringr, purrr, tibble, methods, knitr, igraph, readr, stats, magrittr, rlang
System Requirements
URL

Suggests	rmarkdown, testthat, BiocStyle
Linking To
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Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package	ZygosityPredictor_1.7.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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