hibayes
CRANhibayesMaRDI QIDQ88626FDOQ88626
Individual-Level, Summary-Level and Single-Step Bayesian Regression Model
Xiaolei Liu, Haohao Zhang, Lilin Yin
Last update: 20 February 2024
Copyright license: GNU General Public License, version 3.0
Software version identifier: 2.0.0, 1.0.0, 1.0.1, 1.1.0, 3.0.0, 3.0.1, 3.0.2, 3.0.3
A user-friendly tool to fit Bayesian regression models. It can fit 3 types of Bayesian models using individual-level, summary-level, and individual plus pedigree-level (single-step) data for both Genomic prediction/selection (GS) and Genome-Wide Association Study (GWAS), it was designed to estimate joint effects and genetic parameters for a complex trait, including: (1) fixed effects and coefficients of covariates, (2) environmental random effects, and its corresponding variance, (3) genetic variance, (4) residual variance, (5) heritability, (6) genomic estimated breeding values (GEBV) for both genotyped and non-genotyped individuals, (7) SNP effect size, (8) phenotype/genetic variance explained (PVE) for single or multiple SNPs, (9) posterior probability of association of the genomic window (WPPA), (10) posterior inclusive probability (PIP). The functions are not limited, we will keep on going in enriching it with more features. References: Meuwissen et al. (2001) <doi:10.1093/genetics/157.4.1819>; Gustavo et al. (2013) <doi:10.1534/genetics.112.143313>; Habier et al. (2011) <doi:10.1186/1471-2105-12-186>; Yi et al. (2008) <doi:10.1534/genetics.107.085589>; Zhou et al. (2013) <doi:10.1371/journal.pgen.1003264>; Moser et al. (2015) <doi:10.1371/journal.pgen.1004969>; Lloyd-Jones et al. (2019) <doi:10.1038/s41467-019-12653-0>; Henderson (1976) <doi:10.2307/2529339>; Fernando et al. (2014) <doi:10.1186/1297-9686-46-50>.
- Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps
- Whole-Genome Regression and Prediction Methods Applied to Plant and Animal Breeding
- Extension of the bayesian alphabet for genomic selection
- Bayesian LASSO for Quantitative Trait Loci Mapping
- Polygenic Modeling with Bayesian Sparse Linear Mixed Models
- Simultaneous Discovery, Estimation and Prediction Analysis of Complex Traits Using a Bayesian Mixture Model
- Improved polygenic prediction by Bayesian multiple regression on summary statistics
- A Simple Method for Computing the Inverse of a Numerator Relationship Matrix Used in Prediction of Breeding Values
- A class of Bayesian methods to combine large numbers of genotyped and non-genotyped animals for whole-genome analyses
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