Overview | Data licensing disclaimer | Installation | From Bioconductor devel (current installation method) | From Bioconductor release (after the next Bioconductor release) | From GitHub (latest development version) | Quick start | Step 1 -- Download CTD data | Step 2 -- Import into ctdR | Which CTD release did I use? | Step 3 -- Run enrichment analysis | Prepare your gene list | Shared output schema | Over-Representation Analysis (ORA) | Gene Set Enrichment Analysis (GSEA) | End-to-end example with real RNA-seq data (GSE311566) | Real-data GSEA | Real-data ORA | CAMERA (competitive test with inter-gene correlation) | GSVA (per-sample scoring) | Visualizing results | Adjusting for multiple testing | Gene set size filters and background universe | The background universe is the choice that matters most | Why the size thresholds are what they are | And why there is no upper limit | What that costs, and how to read around it | Choosing among the four methods | Interoperability with existing Bioconductor infrastructure | Reading a CTD file the BiocIO way | Handing the CTD gene sets to another engine | Naming and scope: the "CTD" acronym | Updating the CTD data | References | Session info