DOI: 10.18129/B9.bioc.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 (from within R, enter citation("ZygosityPredictor")):


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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
Suggests knitr, rmarkdown, testthat, BiocStyle
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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
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Bioc Package Browser https://code.bioconductor.org/browse/ZygosityPredictor/
Package Short Url https://bioconductor.org/packages/ZygosityPredictor/
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