Guides

Practical guides for computation that has to survive contact with real data.

This section collects longer-form walkthroughs that go beyond links and notes. The published guides are meant to be usable references. The rest are visible now so the site has a stable place for what is coming next.

Available now

Published guide

Bulk RNA-seq

An opinionated bulk RNA-seq guide for human and mouse studies, split into upstream work up to the count table and downstream analyses that help you extract more biology after differential expression.

bulk RNA-seqhumanmouseDESeq2nf-coreNextflowtranscriptomics

Next up

Metagenomics

Coming soon

Coming soon: guide-oriented workflows for shotgun metagenomics design, QC, assembly-free profiling, and interpretation.

metagenomicsmicrobiome

Phylogenomics

Coming soon

Coming soon: practical phylogenomics strategy for marker choice, tree building, QC, and defensible interpretation.

phylogenomicsevolution

Codex

Coming soon

Coming soon: how I structure Codex for research-heavy engineering, review loops, and reproducible analysis work.

codexworkflowautomation