Saez Lab

decoupleR

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

decoupler-py

Python package to perform enrichment analysis from omics data.

pypath

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

liana-py

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

OmnipathR

R client for the OmniPath web service

CollecTRI

Gene regulatory network containing signed transcription factor-target gene interactions

mistyR

Multiview Intercellular SpaTial modeling framework

omnipath

Python client for the OmniPath web service

corneto

CORNETO: A Unified Omics-Driven Framework for Network Inference

CellNOptR

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

PHONEMeS

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

Factor_COSMOS

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

flop

FunctionaL Omics Processing platform

MetaProViz

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

DOT

DOT

FUNKI

FUNctional analysis worKflows Interface

VisiumMS

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

neo4j-utils

Rich interface on top of the official Neo4j driver

astromouse

Spatial space data from mouse

ccc_protocols

LIANA x Tensor-cell2cell Protocols

metalinks_web

Web interface to allow contextualization of metalinksKG

CRCDiet

CRCDiet

GNNClinicalOutcomePrediction

helminth_inf

Code used for the analysis of GACs and non-GACs in spatial transcriptomics data

lianaplus_manuscript

MetalinksDB

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

networkcommons

PROMISE_lung_multiomics

Lung Cancer Multiomics Dataset including WGS+metaG+RNASeq

pypath-common

Code shared across pypath modules