GBScleanR
This is the development version of GBScleanR; for the stable release version, see GBScleanR.
Error correction tool for noisy genotyping by sequencing (GBS) data
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Tomoyuki Furuta <f.tomoyuki at okayama-u.ac.jp>
citation("GBScleanR")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("GBScleanR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | GeneticVariability, Genetics, HiddenMarkovModel, QualityControl, SNP, Sequencing, Software |
| Version | 2.1.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 years) |
| License | GPL-3 + file LICENSE |
| Depends | SeqArray |
| Imports | stats, utils, methods, ggplot2, tidyr, expm, Rcpp, RcppParallel, gdsfmt |
| System Requirements | GNU make, C++11 |
| URL | https://github.com/tomoyukif/GBScleanR |
| Bug Reports | https://github.com/tomoyukif/GBScleanR/issues |
See More
| Suggests | BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown |
| Linking To | Rcpp, RcppParallel |
| 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/GBScleanR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GBScleanR |
| Package Short Url | https://bioconductor.org/packages/GBScleanR/ |
| Package Downloads Report | Download Stats |