GBScleanR
This is the development version of GBScleanR; for the stable release version, see GBScleanR.
All Bioconductor versions of GBScleanR
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15
Error correction tool for noisy genotyping by sequencing (GBS) data
Bioconductor version: 3.24 · Package version: 2.7.4
GBScleanR is a package for quality check, filtering, and error correction of genotype data derived from next generation sequcener (NGS) based genotyping platforms. GBScleanR takes Variant Call Format (VCF) file as input. The main function of this package is `estGeno()` which estimates the true genotypes of samples from given read counts for genotype markers using a hidden Markov model with incorporating uneven observation ratio of allelic reads. This implementation gives robust genotype estimation even in noisy genotype data usually observed in Genotyping-By-Sequnencing (GBS) and similar methods, e.g. RADseq. The current implementation accepts genotype data of a diploid population at any generation of multi-parental cross, e.g. biparental F2 from inbred parents, biparental F2 from outbred parents, and 8-way recombinant inbred lines (8-way RILs) which can be refered to as MAGIC population.
Author: Tomoyuki Furuta [aut, cre] 
Maintainer: Tomoyuki Furuta <f.tomoyuki at okayama-u.ac.jp>
Citation
From within R, enter citation("GBScleanR"):
Tomoyuki Furuta. GBScleanR: Error correction tool for noisy genotyping by sequencing (GBS) data. doi:10.18129/B9.bioc.GBScleanR, R package version 2.7.4, https://bioconductor.org/packages/GBScleanR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("GBScleanR")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 2.7.4 |
| License | GPL-3 + file LICENSE |
| URL | https://github.com/tomoyukif/GBScleanR |
| Bug Reports | https://github.com/tomoyukif/GBScleanR/issues |
| System Requirements | GNU make, C++11 |
| Last updated | 2026-07-28 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4 years) |
| Downloads rank | 1801 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneticVariability, Genetics, HiddenMarkovModel, QualityControl, SNP, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/GBScleanR/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GBScleanR")| Basic usage of GBScleanR | HTML | R Script |
| Reference Manual |
Download
Follow the installation instructions to use this package in your R session.
| Source package | GBScleanR_2.7.4.tar.gz |
| Windows binary (x86_64) | GBScleanR_2.7.4.zip |
| macOS binary (arm64) | GBScleanR_2.7.4.tgz |
| macOS binary (x86_64) | GBScleanR_2.7.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GBScleanR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GBScleanR |
| Package Downloads Report | Download Stats |
Dependencies
Depends: SeqArray
Imports: stats, utils, methods, ggplot2, tidyr, expm, Rcpp, RcppParallel, gdsfmt
LinkingTo: Rcpp, RcppParallel
Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown