ZygosityPredictor
This is the released version of ZygosityPredictor; for the devel version, see ZygosityPredictor.
Package for prediction of zygosity for variants/genes in NGS data
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| Usage | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, FunctionalPrediction, GenePrediction, Software, SomaticMutation |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 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 |
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_1.12.0.tar.gz |
| Windows Binary (x86_64) | ZygosityPredictor_1.12.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | ZygosityPredictor_1.12.0.tgz |
| macOS Binary (sonoma-arm64) | ZygosityPredictor_1.12.0.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 |