# 01 Overview

## Quick Answer
EVd3x links miRNA, mRNA, protein, pathway, cell, communication, and disease evidence into one analysis workspace. It is optimized for exploratory EV cargo research, not clinical diagnosis. Interactive views may be capped for speed, but provenance and export metadata are included for traceability.

## What this does
EVd3x maps query molecules into a graph, overlays EV evidence, and connects downstream modules: node details, collective expression, cell specificity, cell communication, ligand-receptor analysis, pathway enrichment, and disease association aggregation.

## Inputs
- Query string (single molecule or multi-molecule system list)
- Direction selection (`Both`, `Downstream`, `Upstream`)
- Top-N and tab-specific caps

## Outputs
- Cytoscape network elements
- Module-specific tables and graphs
- Export bundle (CSV and graph files)
- Optional chat planner action plans (`/api/chat`) that execute UI actions
- Assistant responses expand within the bottom command bar and shrink the main view rather than overlaying it.

## How calculated
Each module applies its own method with explicit processing notes. Pathway enrichment uses hypergeometric testing with BH-FDR. Disease aggregation uses canonical `Disease_ID` grouping. Communication modules expose scoring metadata.

Chat planning is deterministic and API-grounded; assistant plans execute EVd3x actions without altering scientific calculations.

## What to download
Use the full export ZIP for reproducible downstream analysis, plus graph PNG/SVG files for figures.

## Known limits
Caps and truncation can affect first-render views. Exports and processing notes are required for interpretation of dense queries.