VIGoR: Variational Bayesian Inference for Genome-Wide Regression
Genome-wide regression using a number of genome-wide markers as predictors is now widely used for genome-wide association mapping and genomic prediction. We developed novel software for genome-wide regression which we named VIGoR (variational Bayesian inference for genome-wide regression). Variation...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Ubiquity Press
2016-04-01
|
| Series: | Journal of Open Research Software |
| Subjects: | |
| Online Access: | http://openresearchsoftware.metajnl.com/articles/80 |
| _version_ | 1818560635901837312 |
|---|---|
| author | Akio Onogi Hiroyoshi Iwata |
| author_facet | Akio Onogi Hiroyoshi Iwata |
| author_sort | Akio Onogi |
| collection | DOAJ |
| description | Genome-wide regression using a number of genome-wide markers as predictors is now widely used for genome-wide association mapping and genomic prediction. We developed novel software for genome-wide regression which we named VIGoR (variational Bayesian inference for genome-wide regression). Variational Bayesian inference is computationally much faster than widely used Markov chain Monte Carlo algorithms. VIGoR implements seven regression methods, and is provided as a command line program package for Linux/Mac, and as a cross-platform R package. In addition to model fitting, cross-validation and hyperparameter tuning using cross-validation can be automatically performed by modifying a single argument. VIGoR is available at https://github.com/Onogi/VIGoR. The R package is also available at https://cran.r-project.org/web/packages/VIGoR/index.html. |
| first_indexed | 2024-12-14T00:40:49Z |
| format | Article |
| id | doaj.art-e62b696345c4463da031a754f4b9a6c7 |
| institution | Directory Open Access Journal |
| issn | 2049-9647 |
| language | English |
| last_indexed | 2024-12-14T00:40:49Z |
| publishDate | 2016-04-01 |
| publisher | Ubiquity Press |
| record_format | Article |
| series | Journal of Open Research Software |
| spelling | doaj.art-e62b696345c4463da031a754f4b9a6c72022-12-21T23:24:24ZengUbiquity PressJournal of Open Research Software2049-96472016-04-0141e11e1110.5334/jors.8071VIGoR: Variational Bayesian Inference for Genome-Wide RegressionAkio Onogi0Hiroyoshi Iwata1Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of TokyoDepartment of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of TokyoGenome-wide regression using a number of genome-wide markers as predictors is now widely used for genome-wide association mapping and genomic prediction. We developed novel software for genome-wide regression which we named VIGoR (variational Bayesian inference for genome-wide regression). Variational Bayesian inference is computationally much faster than widely used Markov chain Monte Carlo algorithms. VIGoR implements seven regression methods, and is provided as a command line program package for Linux/Mac, and as a cross-platform R package. In addition to model fitting, cross-validation and hyperparameter tuning using cross-validation can be automatically performed by modifying a single argument. VIGoR is available at https://github.com/Onogi/VIGoR. The R package is also available at https://cran.r-project.org/web/packages/VIGoR/index.html.http://openresearchsoftware.metajnl.com/articles/80Linear regression, variational Bayesian inference, genome-wide association, genomic prediction, variable selection |
| spellingShingle | Akio Onogi Hiroyoshi Iwata VIGoR: Variational Bayesian Inference for Genome-Wide Regression Journal of Open Research Software Linear regression, variational Bayesian inference, genome-wide association, genomic prediction, variable selection |
| title | VIGoR: Variational Bayesian Inference for Genome-Wide Regression |
| title_full | VIGoR: Variational Bayesian Inference for Genome-Wide Regression |
| title_fullStr | VIGoR: Variational Bayesian Inference for Genome-Wide Regression |
| title_full_unstemmed | VIGoR: Variational Bayesian Inference for Genome-Wide Regression |
| title_short | VIGoR: Variational Bayesian Inference for Genome-Wide Regression |
| title_sort | vigor variational bayesian inference for genome wide regression |
| topic | Linear regression, variational Bayesian inference, genome-wide association, genomic prediction, variable selection |
| url | http://openresearchsoftware.metajnl.com/articles/80 |
| work_keys_str_mv | AT akioonogi vigorvariationalbayesianinferenceforgenomewideregression AT hiroyoshiiwata vigorvariationalbayesianinferenceforgenomewideregression |