Software & Tools
Open-source tools and databases developed by the Saez Lab
BioChatter
A platform for the biomedical application of Large Language Models
ToolBioCypher
A unifying framework for biomedical research knowledge graphs
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
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
ToolMISTy
Explainable machine learning models for single-cell, highly multiplexed, spatially resolved data
ToolNetworkCommons
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
Database