ZygosityPredictor
Package for prediction of zygosity for variants/genes in NGS data
Bioconductor version: Release (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>
citation("ZygosityPredictor")):
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")| ZygosityPredictor_Usage | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
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 |
| Linking To | |
| Suggests | knitr, rmarkdown, testthat, BiocStyle |
| System Requirements | |
| Enhances | |
| URL |
See More
| 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 |
| Old Source Packages for BioC 3.17 | Source Archive |