# Analysis Modules

This is the module-by-module reference for EVd3x.

## Pathway

### Input
- Active genes in the current state
- `gene_pathways.parquet`
- Active filters (p-value threshold, source toggles, keyword)

### Output
- Filtered pathway rows for UI review
- Full pathway export rows

### Boundary
- Pathway enrichment is annotation-level context for follow-up, not pathway activity proof.

## Disease

### Input
- Disease association rows linked to the active state
- Canonical grouping keys (`Disease_ID`)

### Output
- Ranked disease groups and support summaries
- Full disease association exports

### Boundary
- Disease scores are prioritization signals, not causal inference.

## Cell Specificity

### Input
- Cell specificity and expression context tables
- Active molecule state and selected limits

### Output
- Ranked cell-context table
- Exportable cell-context support rows

### Boundary
- Cell ranking reflects curation and query context, not measured abundance in your sample.

## Cell Communication and LR

### Input
- `cell_communication.parquet`
- `ligand_receptor_pairs_full.parquet`
- Selected sender/receiver context

### Output
- Candidate communication links
- Ligand-receptor pair tables and heatmaps
- Exportable communication rows

### Boundary
- These are candidate communication pathways for review, not proof of EV-mediated transfer.

## EV Evidence

### Input
- `ev_evidence.parquet`
- Linked publication and provenance fields

### Output
- Source-attributed EV evidence rows
- Machine-readable EV evidence export

### Boundary
- EV rows support reported detectability and traceability, not abundance or cell-of-origin assignment.

## PPI

### Input
- `string_interactions.parquet`
- Active threshold and expansion settings

### Output
- Protein-protein interaction neighborhood rows
- Expandable PPI network view and export

### Boundary
- PPI context supports ranking and triage; it does not establish mechanism on its own.

## Suggested review order

1. Summary
2. EV Evidence
3. Pathway
4. Disease
5. Cell Communication and LR
6. PPI