Software & Tools
Open-source tools and databases developed by the Saez Lab
Featured
BioChatter
A platform for the biomedical application of Large Language Models
DatabaseBioCypher
A unifying framework for biomedical research knowledge graphs
ToolCellNOpt
Create logic models of signaling networks and train them with perturbation data
ToolCollecTRI
Collection of Transcriptional Regulatory Interactions
DatabaseCORNETO
Unified framework for network inference problems
ToolCOSMOS
Mechanistic integration of multi-omics with prior knowledge into causal networks
TooldecoupleR
Estimate biological activities from omics data
DatabaseDOT
An optimization framework for transferring cell features from a reference data to spatial omics
ToolLIANA+
Framework to infer inter- and intra-cellular signalling from single-cell and spatial omics
ToolMISTy
Explainable machine learning models for single-cell, highly multiplexed, spatially resolved data
DatabaseNetworkCommons
Platform for network inference based on prior knowledge and omics data
ToolOmniPath
Molecular prior knowledge from more than 170 databases. Pathways, intercellular communication and more.
DatabasePROGENy
Collection of target genes (footprints) of signaling pathways
DatabaseAll Tools
BioCypher
A unifying framework for biomedical research knowledge graphs
ToolCellNOpt
Create logic models of signaling networks and train them with perturbation data
ToolCORNETO
Unified framework for network inference problems
ToolCOSMOS
Mechanistic integration of multi-omics with prior knowledge into causal networks
ToolDOT
An optimization framework for transferring cell features from a reference data to spatial omics
ToolLIANA+
Framework to infer inter- and intra-cellular signalling from single-cell and spatial omics
ToolNetworkCommons
Platform for network inference based on prior knowledge and omics data
ToolBioServices
Python package to access Bioinformatics Web Services.
ToolBirewire
R package for the randomisation of bipartite graphs.
ToolCARNIVAL
Find causal paths upstream of transcription factors in signaling networks from transcriptomics
ToolDREAMTools
Code used in the scoring of DREAM challenges.
ToolGDSCTools
Python library dedicated to the study pharmacogenomic relationships.
Toollipyd
Python module for lipidomics LC MS/MS data analysis
ToolMEIGO
Global optimization toolbox including metaheuristic and Bayesian methods.
ToolocEAn
Metabolic enzyme enrichment analysis
ToolPHONEMeS
Build causal signaling networks from untargeted mass-spectrometry Phosphoproteomics and prior knowledge
ToolSLAPenrich
R package to identify pathway-level enrichments of genetic alterations.
ToolAll Databases
BioChatter
A platform for the biomedical application of Large Language Models
DatabaseCollecTRI
Collection of Transcriptional Regulatory Interactions
DatabaseOmniPath
Molecular prior knowledge from more than 170 databases. Pathways, intercellular communication and more.
DatabasePROGENy
Collection of target genes (footprints) of signaling pathways
DatabaseMetalinksDB
Database of protein-metabolite and small molecule ligand-receptor interactions
Database