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