Protocols
Tutorials and protocols are different things. A tutorial
teaches you one function (what CPP or ShapModel does and how to call it).
A protocol teaches you a workflow: it answers a single biological question
from start to finish and, above all, builds the mental model for when and why
to reach for each tool. Where a protocol uses a function, it links to that
function’s tutorial for the mechanics instead of repeating them, so the two stay
distinct with no overlap.
The protocols catalog at a glance — each tile is the headline figure of one protocol; click it to open that protocol.
The mental model. AAanalysis turns a biological question into an interpretable comparison. You bring two (or more) groups of sequences; CPP reads out the signature (the physicochemical features, resolved by position, that distinguish them), and the rest of the pipeline helps you sample fairly, engineer features, select what matters, predict, explain, and check that the signal is real. The catalog follows that data flow, opening with the CPP signature, then an exploratory no-label first look, and on through sampling, feature engineering, selection, modelling, explanation, and validation.