README.md

HLA Genotype Imputation with Attribute Bagging

Kernel Version: 1.5

GPLv3 GNU General Public License, GPLv3

Availability Years-in-BioC Build Status Build status codecov.io

Features

HIBAG is a state of the art software package for imputing HLA types using SNP data, and it relies on a training set of HLA and SNP genotypes. HIBAG can be used by researchers with published parameter estimates instead of requiring access to large training sample datasets. It combines the concepts of attribute bagging, an ensemble classifier method, with haplotype inference for SNPs and HLA types. Attribute bagging is a technique which improves the accuracy and stability of classifier ensembles using bootstrap aggregating and random variable selection.

Bioconductor Package

Release Version: 1.26.1

http://www.bioconductor.org/packages/HIBAG/

Changes in Bioconductor Version (since v1.26.0, Y2020):

Changes in Bioconductor Version (since v1.14.0, Y2017):

Changes in Bioconductor Version (since v1.3.0, Y2013):

Package Author & Maintainer

Dr. Xiuwen Zheng

Pre-fit Model Download

Citation

Zheng, X. et al. HIBAG-HLA genotype imputation with attribute bagging. Pharmacogenomics Journal 14, 192-200 (2014). doi: 10.1038/tpj.2013.18

Zheng, X. (2018) Imputation-Based HLA Typing with SNPs in GWAS Studies. In: Boegel S. (eds) HLA Typing. Methods in Molecular Biology, Vol 1802. Humana Press, New York, NY. doi: 10.1007/978-1-4939-8546-3_11

Installation

source("http://bioconductor.org/biocLite.R")
biocLite("HIBAG")
library("devtools")
install_github("zhengxwen/HIBAG")

The install_github() approach requires that you build from source, i.e. make and compilers must be installed on your system -- see the R FAQ for your operating system; you may also need to install dependencies manually.

Acceleration

CPU with Intel Intrinsics

GPU with OpenCL

Archive

https://github.com/zhengxwen/Archive/tree/master/HIBAG

https://bioconductor.org/about/release-announcements



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HIBAG documentation built on March 24, 2021, 6 p.m.