Reciprocal BLUP

Reciprocal BLUP for multi-omics data: integrating genome, metabolome, and microbiome in soybean

This repository contains all data and analysis scripts used in the study.
Both the datasets and R Markdown scripts are openly available for reproducibility.

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📂 Data Availability

Folder: data_reciprocal/

File	Description
blup_control.rds	Multi-omics data under control conditions
blup_drought.rds	Multi-omics data drought-stress conditions

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📜 Code Description

Folder: script_reciprocal/

Script	Description
a1_model_1_3.Rmd	Feature selection and model fitting using Model 1 and Model 3
a2_model_2_4.Rmd	Feature selection using Model 2 and Model 4
b1_histgram.Rmd	Plot histograms for selected feature distributions
b2_cor.Rmd	Evaluate omics features prediction
b3_features.Rmd	Summary and visualization of selected features
c1_percent.Rmd	Phenotype prediction with reduced metabolome features
c2_percent_micro.Rmd	Phenotype prediction with reduced microbiome features
c3_phenotype_result.Rmd	Visualization and interpretation of phenotype prediction results

Each .Rmd file can be executed sequentially using rmarkdown::render().
Please ensure all required R packages are installed before running the scripts.

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🔍 Overview

This repository provides the full set of scripts and data used in the Reciprocal BLUP study.
The materials here are shared for transparency, reproducibility, and reuse.
Researchers are encouraged to adapt and extend the code for related analyses.

If you use this repository, please cite the associated paper

Reciprocal BLUP: A Predictability-Guided Multi-Omics Framework for Plant Phenotype Prediction (https://doi.org/10.3390/plants15010017)

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