Shipping a 20 GB Atlas
A Shiny dashboard over four single-cell objects would not deploy and could not run. The fix was how the matrix was stored, not how plots were drawn.
Read more →
The Lab Notebook
Unpolished discoveries, learning moments, and scientific musings from a PhD journey.
16 posts found
From Slowing to Stopping IPF progression: Where Are We Now?
Where IPF drug development stands today—from slowing FVC decline to precision targets, inhaled delivery, and disease modification.
Read more →Modeling Disease Progression in Single Cells: When to Reach for LM, GLM, or GAM
A practical, coffee-fueled guide to choosing between linear, generalized linear, and generalized additive models for single-cell gene expression analysis.
Read more →
The "Why" Behind Various Sequencing Modalities
Understanding why different sequencing modalities exist: each optimizes different tradeoffs in resolution, scale, sensitivity, cost, and interpretability to answer specific biological questions.
Read more →
DESeq2 vs edgeR: A Practical Guide for RNA-seq Differential Expression
A practical, under-the-hood guide for choosing between DESeq2 and edgeR for RNA-seq differential expression analysis, covering statistical foundations, design specification, and best practices.
Read more →
How to Choose Between ANOVA and Kruskal-Wallis: A Practical Guide
A practical guide to choosing between ANOVA and Kruskal-Wallis tests, with decision flowcharts, worked examples, and mathematical foundations.
Read more →Scanpy `standard_scale`: var vs group — finally clear (with manual calculations)
Deep-dive into standard_scale='var' vs 'group' in Scanpy heatmaps, dotplots & matrixplots — complete with step-by-step math and when to choose each.
Read more →How the Lung Epithelium Repairs Itself: AT2 Cells, Wnt Niches, and Timing
A reference-heavy tour of AT2 facultative stem cells and how Wnt signaling supports alveolar repair—until it doesn’t.
Read more →The Wnt Paradox: How the Same Pathway Can Heal and Harm the Lung
Exploring the dual role of Wnt/β-catenin signaling in pulmonary fibrosis—why activation sometimes heals and sometimes harms.
Read more →