README.md

Project Overview

This repository contains the entire bioinformatic pipeline and data for the ABCC Group Project Group 10.

Paper ID = 1

Title = Adaptive laboratory evolution of native methanol assimilation in Saccharomyces cerevisiae

Repository Structure

ABCC_Workflow/
├── data/                                      <-- Data Storage Directory
│   ├── Clean_Proteomics_data.csv              <-- Clean proteomics dataset
│   ├── Metadata_samples.csv                   <-- Sample metadata for samples provided by the paper
│   ├── DEGs_control_vs_evolved_padj0.01.xlsx  <-- Differential expression results
│   ├── clusterProfiler_GO_enrichment.xlsx     <-- GO enrichment results (clusterProfiler)
│   ├── YeastMine_GO_enrichment_UP.html        <-- GO enrichment - UP-regulated (YeastMine)
│   └── YeastMine_GO_enrichment_DOWN.html      <-- GO enrichment - DOWN-regulated (YeastMine)
│
├── scripts/                                   <-- Source Code Directory
│   ├── G10_full_workflow.Rmd                  <-- Full analysis workflow (Bash + R)
│   └── Rshiny_app.R                           <-- Interactive visualization (RShiny)
│
├── .gitignore
└── README.md