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Learning The Basics of Phylogenetic Analysis

🧬🔬 Explore phylogenetic analysis from genome to tree! Basic workflow with R/Bioconductor. Learnt to work with large genomic dataset. Extract 16S rRNA from 10K+ E.coli strains using dataset dehydrate, barrnap for extraction, rapidNJ for tree building & FigTree for visualization.

By Ken Koon Wong in r R phylgenetic analysis bioconductor DECIPHER alignment ape barrnap rapidnj figtree ggtree

August 31, 2025

Learning Antimicrobial Resistance (AMR) genes with Bioconductor

Instead of flashcards, we Rube Goldberg’d this with Bioconductor! Analyzed 3,280 E. coli genomes from NCBI, detecting ESBL genes in 84.4% of samples. CTX-M-15 was most common. Helped us understand gene nomenclature and sequence analysis! 📊🔬

By Ken Koon Wong in r R bioconductor biostring amr antimicrobiral resistance esbl blactx-m blashv blatem

August 15, 2025

Creating A Question Bank Using Google Sheet, Plumber, and Digital Ocean Droplet

Learn how to build a flash-card style question bank using Google Sheets as storage, R’s Plumber API, and host it on a Digital Ocean droplet—step-by-step setup, deployment, and tips.

By Ken Koon Wong in r R meded medical education plumber google sheet digitial ocean droplet

June 18, 2025

From Math to Code: Building GAM with Penalty Functions From Scratch

Enjoyed learning penalized GAM math. Built penalty matrices, optimized λ using GCV, and implement our own GAM function. Confusing? Yes! Rewarding? Oh yes!

By Ken Koon Wong in r R gam penalty gcv matrix calculus calculus derivative reimann sum taylor series

June 11, 2025

Understanding Basis Spline (B-spline) By Working Through Cox-deBoor Algorithm

I finally understood B-splines by working through the Cox-deBoor algorithm step-by-step, discovering they’re just weighted combinations of basis functions that make non-linear regression linear. What surprised me is going through Bayesian statistics really helped me understand the engine behind the model! Will try this again in the future!

By Ken Koon Wong in r R bspline cox-deboor spline bs

June 3, 2025

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Quote of the Week

Success is not final; failure is not fatal: It is the courage to continue that counts.

Written by Winston S. Churchill

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