Saez Lab

liana-py

LIANA+: an all-in-one framework for cell-cell communication

MetalinksDB

cosmosR

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

Factor_COSMOS

Formatting NCI60 data into cosmos ready inputs and generation of testable hypothesis connecting cell-line specific TF and metabolic deregulations.

MetaProViz

R-package to perform metabolomics pre-processing, differential metabolite analysis, metabolite clustering and custom visualisations.

OmnipathR

R client for the OmniPath web service

corneto

CORNETO: A Unified Omics-Driven Framework for Network Inference

python-project

Python project template

GNNClinicalOutcomePrediction

pypath-dlmanager

Download manager for pypath

VisiumHGSC

Analysis of HGSC tissue micro-arrays with Visium and Misty

decoupler-py

Python package to perform enrichment analysis from omics data.

networkcommons

GDSC_ML_tutorial

tutorial to train a ridge regression on RNAseq or TF activities

FUNKI

FUNctional analysis worKflows Interface

VisiumMS

Study of Multiple Sclerosis(MS) using paried snRNA-seq and Visium transcriptmics datasets.

lianaplus_manuscript

pypath

Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.

flop

FunctionaL Omics Processing platform

ccc_protocols

LIANA x Tensor-cell2cell Protocols

PHONEMeS

PHONEMeS (PHOsphorylation NEtworks for Mass Spectrometry) is an R package to model signalling networks based on untargeted phosphoproteomics

CRCDiet

CRCDiet

DOT

DOT

CollecTRI

Gene regulatory network containing signed transcription factor-target gene interactions

omnipath

Python client for the OmniPath web service

PROMISE_lung_multiomics

Lung Cancer Multiomics Dataset including WGS+metaG+RNASeq

metalinks_web

Web interface to allow contextualization of metalinksKG

decoupleR

R package to infer biological activities from omics data using a collection of methods.

astromouse

Spatial space data from mouse

CellNOptR

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data.