Advanced guides

Methods and interpretation
Inputs and configuration
Reports and worked examples
Reference

Use these guides when you need to understand a method or change the default workflow. For a first run, follow Get started.

Methods and interpretation

Statistical analysis: gene-set tests, category inference and the limits of comparisons.
How lisaR works: dictionaries, categories and resources.
Category guide: plot variants and their meaning.
Dictionary construction: how the saved assignments were produced.

Inputs and configuration

Extended R workflow: input objects, multiple DE analyses, contrasts and report options.
Prepare DE inputs: input conventions and provenance.
Resources and provenance: membership resources and their registration.
Custom dictionaries: your own categories and supercategories.
Installation details: optional dependencies, local environments and installation troubleshooting.

Reports and worked examples

Reports and figures: additional products and saved result workflows.
Shiny app: explore saved results and generate selected figures.
Riaz PRE and ON: the complete prepared study.
CPTAC proteomics: a proteomic example.
Synthetic example: a self-contained offline demonstration.

Reference