Applications of the Soybean Expression Atlas in Genomics and Transcriptomics Research

This repository is part of the chapter titled "Applications of the Soybean Expression Atlas in Genomics and Transcriptomics Research", which explores the use of the soybean expression atlas in genomics and transcriptomics studies. The chapter provides an in-depth overview of how to use transcriptomic data from the Soybean Expression Atlas to understand the molecular mechanisms behind important traits in soybean, such as stress tolerance and disease resistance.

Contents

This repository includes the following:

• Data: Raw data and processed datasets used in the analysis, including RNA-seq and Genomic Association Studies (GWAS) data and related metadata.
• Scripts: R and Python scripts used to process and analyze the soybean transcriptomic and genomic data.
• Analysis Results: Results of analyses, such as differential expression, co-expression networks, and gene ontology enrichment.
• Figures: Visualizations such as heatmaps, volcano plots, and gene expression comparisons.

Subdirectories

• cTruncatumAnalysis: Contains data and R scripts for co-expression network analysis and gene ontology enrichment. Code and analysis by @dayana-turquetti
• hGlycines: Includes genetic association data, transcriptome data, and a Python script for differential expression analysis.

How to Use

1. Clone this repository:

   git clone https://github.com/aluizakarl/dataAnalysisSEA.git
   

2. Navigate to a specific directory:

cd dataAnalysisSEA/cTruncatumAnalysis

or

cd dataAnalysisSEA/hGlycines