How remynicolle/coregnet-bioc works
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: classes.R Regulatory network · display.R Network display · masterRegulators.R Regulator influence · coRegnet.R Co-coregulators
Components 14
Network inference
- hLICORN inference
R/netInference.R - Regulatory network
R/classes.R - LICORN native routine
src/comblicorn.c
Network analysis
- Regulator influence
R/masterRegulators.R - Co-coregulators
R/coRegnet.R - Master regulators
R/masterRegulators.R - Evidence handling
R/evidences.R - Network refinement
R/netInference.R
Interactive display
- Network display
R/display.R - Shiny interface
R/display.R - Cytoscape renderer
inst/www/js/cy.js
Package resources
- Bundled datasets
data
Other components
- Analyst
- Expression data
Connections 21
- 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