reader is a toolkit for organizing experiment directories and running config-driven analysis pipelines over structured assay data. Each experiment has a clear working layout: raw inputs live in inputs/, optional notebooks live in notebooks/, generated results live in outputs/, and a reader/v7 config.yaml describes what should be run.
- Documentation index: complete map of user docs, reference docs, and maintainer docs.
- Getting started: install
reader, verify the environment, and inspect the first experiment. - Preflight, run, verify: deterministic path for inspecting, executing, and checking one experiment.
- Automation and JSON: machine-readable discovery, inspection, and preflight surfaces.
- CLI reference: full command reference.
- Configuring
reader/v7: the public authoring surface for experiment configs. - Repo maintenance: maintainer verification and CI lanes.