Multi-Omics Data Analytics & Practical Training 🧬

This repository showcases a comprehensive suite of bioinformatics workflows, from raw data processing on High-Performance Computing (HPC) clusters to integrated multi-omics downstream analysis. The projects demonstrate proficiency in DNA-Seq, RNA-Seq, ChIP-Seq, and Proteomics.

🎯 Core Competencies & Learning Objectives

💻 High-Performance Computing (HPC) & Bash

• Infrastructure: Proficient in the Linux system and HPC environments for large-scale data processing.
• Job Management: Experienced in job submission, node management, and executing array jobs.
• Automation: Developing Bash scripts for automated bioinformatics pipelines and custom functions.

🧬 DNA Sequencing & Variant Analytics (WES/WGS)

• Primary Analysis: Handling Fastq files, Quality Control (QC), and sequence alignment using Samtools.
• Variant Discovery: Somatic and germline variant calling, including functional annotation and interpretation of Variant Allele Frequency (VAF).
• Practical Output: DNA-Seq Analysis Report.

📊 RNA Sequencing & Differential Expression

• Quantification: Gene quantification from Fastq files, raw read counting, and library normalization.
• Statistical Analysis: Differential Gene Expression (DGE) analysis and data interpretation using R/Bioconductor.
• Pathway Analysis: Performing Gene Set Over-representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA).
• Practical Output: RNA-Seq Analysis Report.

🕯️ Epigenomics & ChIP-Seq Analysis

• Peak Calling: Analyzing regulatory elements using MACS2, including PCR duplicate removal and down-sampling.
• Annotation: Peak annotation in relation to genes and genomic features; Motif enrichment analysis.
• Visualization: Mapping read distributions in regions of interest and visualizing ChIP-Seq peaks.

🧪 Proteomics & Signal Transduction

• Quantitative Proteomics: Standard proteomics analysis and enrichment analysis to study protein-level changes.
• Kinase Activity: Profiling kinase activity and signal transduction pathways (e.g., MAPK pathway) under therapeutic treatment.

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📁 Repository Structure

📂 Genomics & Variant Calling

• DNA-Seq Analysis Report: VAF interpretation and mutation discovery.
• Filtered Variants: High-confidence somatic variants.
• Alignment QC: HPC-generated QC and alignment stats.

📂 Transcriptomics & Epigenomics

• RNA-Seq Analysis Report: DGE and GSEA results.
• ChIP-Seq Analysis Part 1: Filtering and input preparation.
• ChIP-Seq Peak Annotation: Motif analysis and distribution plots.
• Visualisation Report: Integrated epigenetic visualizations.

📂 Proteomics & Theory

• Proteomics Report: Kinase activity and enrichment.
• Theoretical Analysis: Discussion on single-cell vs. bulk technologies and DNA methylation techniques.

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🛠 Bioinformatic Toolset

• Languages: Bash/Shell, R (Bioconductor).
• Genomics: Samtools, BWA, VarScan2, ANNOVAR.
• Epigenomics: MACS2, ChIPseeker, Motif Analysis tools.
• Proteomics: Limma, KSEAapp.
• Environment: High-Performance Computing (HPC) Clusters.