Registration and Call for Abstracts Open for Bioc2024

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 (3.19)

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>

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

Installation

To install this package, start R (version "4.4") 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

Details

biocViews BiomedicalInformatics, FunctionalPrediction, GenePrediction, Software, SomaticMutation
Version 1.3.83
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
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
See More
Suggests rmarkdown, testthat, BiocStyle
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 ZygosityPredictor_1.3.83.tar.gz
Windows Binary ZygosityPredictor_1.3.83.zip (64-bit only)
macOS Binary (x86_64) ZygosityPredictor_1.3.83.tgz
macOS Binary (arm64) ZygosityPredictor_1.3.83.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