EMOAR (End-to-End Multi-Omics Analysis with Reproducible HTML Reporting)

This repository contains interactive HTML reports generated from R for both bulk RNA-seq and single-cell RNA-seq (scRNA-seq) analyses. The purpose of these reports is to provide a fast, visually appealing showcase of R analysis, visualization, and HTML reporting skills, suitable for portfolio and CV presentation.

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Reports

1. Simple Bulk RNA-seq Report

   • HTML file: ../results/bulk_rnaseq_showcase.html

   • Includes:

     • Quality control and filtering
     • Differential expression analysis
     • PCA plot of samples
     • Volcano plot of DE genes (interactive with Plotly)
     • Interactive and browsable tables of results using DT

2. Simple Single-Cell RNA-seq Report

   • HTML file: ../results/scRNAseq_showcase.html

   • Includes:

     • Cell QC and filtering
     • Normalization and HVG selection
     • PCA and UMAP visualizations
     • Interactive marker volcano-like plots (example)
     • Interactive and browsable tables of cell metadata using DT

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Purpose

These reports are designed for quick demonstration purposes:

• Showcase the ability to process and visualize omics data in R
• Produce clean, interactive HTML outputs
• Highlight portfolio/CV presentation style

For full-scale, production-ready RNA-seq analysis pipelines, including batch correction, advanced normalization, and comprehensive differential expression workflows, please refer to the RNA-seq pipeline repository/documentation.