How laurenmbell/networks works
This repository is a collection of research scripts for reconstructing and interrogating multi-omic correlation networks, rather than a packaged application. The broad workflow is to preprocess tissue/metabolite measurements, calculate correlations and FDR tables, then summarize or interrogate network edges and directions. Related scripts cover CSF, FECI, PLS/CPX, and plasma analyses; additional tools map biological node types and reverse inferred edge directions. The README describes the overall purpose, but most scripts appear standalone: excerpts do not establish a shared runtime orchestrator or links between analysis stages, so those connections are not asserted.
Main entry points: CSF-ESP.py CSF edge prediction · reverse_puc.py Reverse PUC
Components 24
CSF analyses
- CSF preprocessing
CSF-CPX/preprocessing.py - CTX preprocessing
CSF-CTX/preprocessing.py - RBN preprocessing
CSF-RBN/preprocessing.py - STR preprocessing
CSF-STR/preprocessing.py - CSF correlations
CSF/compute_correlations.py - CSF FDR tables
CSF/fdr_table.py - CSF properties
CSF/network_property.py
Cross-omic analyses
- FECI analysis
FECI/feci_analysis - FECI CPX analysis
FECI-CPX/pooled_correlation.py - FECI PLS analysis
FECI-PLS/pooled_correlation.py - PLS CPX analysis
PLS-CPX/filter_rename.py - Plasma properties
PLASMA/plasma_analysis/network_prop_table.py
Network interrogation
- CSF edge prediction
CSF_ESP/CSF-ESP.py - Edge sign prediction
CSF_ESP/CSF-brain_edge_signs/edge_sign_prediction.py - Reverse PUC
inverse_puc/reverse_puc.py - Network properties
network_properties_old/network_prop_table.py
Node mapping
- Biological type map
bibc/type_map.py - Tissue edge mapping
bibc/typemap.py - BIBC calculation
bibc/calc_bibc.py - CSF analysis table
CSF_analysis/CSF_analysis_table.py
Metabolomics tools
- Metabolomics EDA
metabolomics_analysis/eda.py - PubChem lookup
metabolomics_analysis/pubchem_rest.py - Duplicate analysis
metabolomics_analysis/duplicate analysis /duplicate_analysis.py
Other components
- Researcher
Connections 2
- Researcher → CSF edge prediction: runs
CSF_ESP/CSF-ESP.py - CSF edge prediction → Reverse PUC: implements method