How to Interpret Your Own CGM Data
A working method for turning a raw Libre or Dexcom export into an ambulatory glucose profile, per-meal response curves, and metrics you can defend — including what the numbers can and cannot tell you.
Tag: python
4 posts
How to Plot Your Own RNA-Seq Data: PCA, Volcano, and Trajectory Graphs
A working guide to turning RNA-seq FASTQs into the handful of plots that matter: sample PCA, distance heatmaps, MA and volcano plots, and longitudinal gene trajectories, with the commands, parameters, and failure modes.
Analyzing Your Own Bulk RNA-Seq Data in Python
A working pipeline from FASTQ files to gene-level counts, differential expression, and enrichment, using salmon, pytximport, and PyDESeq2, with the failure modes specific to blood RNA from a single person.
How to Make Violin Plots of RNA-seq Expression Data
A practical guide to building violin plots from bulk and single-cell RNA-seq counts: which normalization to plot, how to set kernel bandwidth and trimming, and how to read the shapes without fooling yourself.