MSc Module 3: Programming for Biological Data (2026)

Instructor: Haogao GU

Institution: SPH HKU / HKU SPACE

Date: January 2026

Course Overview

This repository contains the comprehensive preparation package for Module 3, tailored for Postgraduate Certificate in Bioinformatics for Medical Laboratory Technologists (MLTs). This plan integrates the "Code-as-Protocol" pedagogical approach.

Quick Start

No software installation is required. We will use Google Colab for our "Dry Lab" sessions. Remember to change runtime to R while using colab (Runtime -> Change runtime type -> R).

• Session 1: Introduction to R (Part 1)

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• Session 2: Introduction to R (Part 2) - Data Frames & I/O

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• Session 3: Introduction to R (Part 3) - Logic & Control Flow

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• Session 4: Introduction to R (Part 4) - Data Visualization

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• Session 5: Hypothesis Testing - T-tests & Normality

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• Session 6: ANOVA & Linear Regression

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• Session 7: Diagnostic Accuracy (ROC Curves)

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• Session 8: Laboratory Quality Control (LJ Charts & Westgard)

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• Session 9: Introduction to Bioconductor (Biostrings)

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• Session 10: Sanger Sequencing Analysis (sangeranalyseR)

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• Session 11: Phylogenetics (MSA & Tree Building)

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• Session 12: Visualization & Reporting (ggtree)

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Assessments

• Assessment 1: R Fundamentals

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• Assessment 2: Biomarker Validation

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• Assessment 3: Sanger Processing

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• Assessment 4: ggtree Visualization

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