# remynicolle/coregnet-bioc architecture

> Architecture diagram of the GitHub repository remynicolle/coregnet-bioc, generated by GitDiagram from its file tree, README and a sample of source files (last updated 2026-09-29). It is an AI-made overview: check details against the source.

- Interactive diagram: https://gitdiagram.com/remynicolle/coregnet-bioc
- Repository: https://github.com/remynicolle/coregnet-bioc

## Overview

CoRegNet is an R/Bioconductor package for inferring and analyzing gene regulatory networks. Its documented workflow takes expression data through hLICORN to a network, then derives regulator influence and co-coregulators and displays the results interactively. The graph also includes documented evidence/refinement and master-regulator capabilities. README workflows support the principal data-flow edges; source excerpts are incomplete, so uncertain internal calls and wiring to packaged datasets are omitted.

Main entry points: [`R/classes.R`](https://github.com/remynicolle/coregnet-bioc/blob/master/R/classes.R) (Regulatory network), [`R/display.R`](https://github.com/remynicolle/coregnet-bioc/blob/master/R/display.R) (Network display), [`R/masterRegulators.R`](https://github.com/remynicolle/coregnet-bioc/blob/master/R/masterRegulators.R) (Regulator influence), [`R/coRegnet.R`](https://github.com/remynicolle/coregnet-bioc/blob/master/R/coRegnet.R) (Co-coregulators)

## Diagram (Mermaid)

```mermaid
flowchart TD

subgraph group_inference["Network inference"]
  node_inference["hLICORN inference<br/>[netInference.R]"]
  node_network["Regulatory network<br/>[classes.R]"]
  node_native["LICORN native routine<br/>[comblicorn.c]"]
end

subgraph group_analysis["Network analysis"]
  node_influence["Regulator influence<br/>[masterRegulators.R]"]
  node_coregulators["Co-coregulators<br/>[coRegnet.R]"]
  node_master["Master regulators<br/>[masterRegulators.R]"]
  node_evidence["Evidence handling<br/>[evidences.R]"]
  node_refinement["Network refinement<br/>[netInference.R]"]
end

subgraph group_display["Interactive display"]
  node_display["Network display<br/>[display.R]"]
  node_shiny["Shiny interface<br/>[display.R]"]
  node_cytoscape["Cytoscape renderer<br/>[cy.js]"]
end

subgraph group_resources["Package resources"]
  node_datasets["Bundled datasets"]
end

node_user(("Analyst"))
node_expression["Expression data"]

node_user -->|"provides"| node_expression
node_expression -->|"infers from"| node_inference
node_inference -->|"produces"| node_network
node_user -->|"requests"| node_influence
node_network -->|"analyzes"| node_influence
node_expression -->|"analyzes"| node_influence
node_user -->|"requests"| node_coregulators
node_network -->|"analyzes"| node_coregulators
node_expression -->|"analyzes"| node_coregulators
node_user -->|"requests"| node_display
node_network -->|"displays"| node_display
node_expression -->|"displays with"| node_display
node_influence -->|"displays with"| node_display
node_display -->|"opens"| node_shiny
node_shiny -->|"renders via"| node_cytoscape
node_user -->|"requests"| node_master
node_network -->|"analyzes"| node_master
node_user -->|"manages"| node_evidence
node_evidence -->|"annotates"| node_network
node_user -->|"requests"| node_refinement
node_network -->|"refines"| node_refinement

click node_inference "https://github.com/remynicolle/coregnet-bioc/blob/master/R/netInference.R"
click node_network "https://github.com/remynicolle/coregnet-bioc/blob/master/R/classes.R"
click node_influence "https://github.com/remynicolle/coregnet-bioc/blob/master/R/masterRegulators.R"
click node_coregulators "https://github.com/remynicolle/coregnet-bioc/blob/master/R/coRegnet.R"
click node_master "https://github.com/remynicolle/coregnet-bioc/blob/master/R/masterRegulators.R"
click node_evidence "https://github.com/remynicolle/coregnet-bioc/blob/master/R/evidences.R"
click node_refinement "https://github.com/remynicolle/coregnet-bioc/blob/master/R/netInference.R"
click node_display "https://github.com/remynicolle/coregnet-bioc/blob/master/R/display.R"
click node_shiny "https://github.com/remynicolle/coregnet-bioc/blob/master/R/display.R"
click node_cytoscape "https://github.com/remynicolle/coregnet-bioc/blob/master/inst/www/js/cy.js"
click node_datasets "https://github.com/remynicolle/coregnet-bioc/tree/master/data"
click node_native "https://github.com/remynicolle/coregnet-bioc/blob/master/src/comblicorn.c"

classDef toneNeutral fill:#f8fafc,stroke:#334155,stroke-width:1.5px,color:#0f172a
classDef toneBlue fill:#dbeafe,stroke:#2563eb,stroke-width:1.5px,color:#172554
classDef toneAmber fill:#fef3c7,stroke:#d97706,stroke-width:1.5px,color:#78350f
classDef toneMint fill:#dcfce7,stroke:#16a34a,stroke-width:1.5px,color:#14532d
classDef toneRose fill:#ffe4e6,stroke:#e11d48,stroke-width:1.5px,color:#881337
classDef toneIndigo fill:#e0e7ff,stroke:#4f46e5,stroke-width:1.5px,color:#312e81
classDef toneTeal fill:#ccfbf1,stroke:#0f766e,stroke-width:1.5px,color:#134e4a
class node_inference,node_network,node_native toneBlue
class node_influence,node_coregulators,node_master,node_evidence,node_refinement toneAmber
class node_display,node_shiny,node_cytoscape toneMint
class node_datasets toneRose
class node_user,node_expression toneIndigo
```

## Components

### Network inference

- [hLICORN inference](https://github.com/remynicolle/coregnet-bioc/blob/master/R/netInference.R): `R/netInference.R`
- [Regulatory network](https://github.com/remynicolle/coregnet-bioc/blob/master/R/classes.R): `R/classes.R`
- [LICORN native routine](https://github.com/remynicolle/coregnet-bioc/blob/master/src/comblicorn.c): `src/comblicorn.c`

### Network analysis

- [Regulator influence](https://github.com/remynicolle/coregnet-bioc/blob/master/R/masterRegulators.R): `R/masterRegulators.R`
- [Co-coregulators](https://github.com/remynicolle/coregnet-bioc/blob/master/R/coRegnet.R): `R/coRegnet.R`
- [Master regulators](https://github.com/remynicolle/coregnet-bioc/blob/master/R/masterRegulators.R): `R/masterRegulators.R`
- [Evidence handling](https://github.com/remynicolle/coregnet-bioc/blob/master/R/evidences.R): `R/evidences.R`
- [Network refinement](https://github.com/remynicolle/coregnet-bioc/blob/master/R/netInference.R): `R/netInference.R`

### Interactive display

- [Network display](https://github.com/remynicolle/coregnet-bioc/blob/master/R/display.R): `R/display.R`
- [Shiny interface](https://github.com/remynicolle/coregnet-bioc/blob/master/R/display.R): `R/display.R`
- [Cytoscape renderer](https://github.com/remynicolle/coregnet-bioc/blob/master/inst/www/js/cy.js): `inst/www/js/cy.js`

### Package resources

- [Bundled datasets](https://github.com/remynicolle/coregnet-bioc/tree/master/data): `data`

### Other components

- **Analyst**
- **Expression data**

## Connections

- Analyst → Expression data: provides
- Expression data → hLICORN inference: infers from
- hLICORN inference → Regulatory network: produces
- Analyst → Regulator influence: requests
- Regulatory network → Regulator influence: analyzes
- Expression data → Regulator influence: analyzes
- Analyst → Co-coregulators: requests
- Regulatory network → Co-coregulators: analyzes
- Expression data → Co-coregulators: analyzes
- Analyst → Network display: requests
- Regulatory network → Network display: displays
- Expression data → Network display: displays with
- Regulator influence → Network display: displays with
- Network display → Shiny interface: opens
- Shiny interface → Cytoscape renderer: renders via
- Analyst → Master regulators: requests
- Regulatory network → Master regulators: analyzes
- Analyst → Evidence handling: manages
- Evidence handling → Regulatory network: annotates
- Analyst → Network refinement: requests
- Regulatory network → Network refinement: refines