Pinned Repositories
CollecTRI
Gene regulatory network containing signed transcription factor-target gene interactions
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.
dorothea
R package to access DoRothEA's regulons
liana
LIANA: a LIgand-receptor ANalysis frAmework
liana-py
LIANA+: an all-in-one framework for cell-cell communication
OmnipathR
R client for the OmniPath web service
progeny
R package for Pathway RespOnsive GENe activity inference
pypath
Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.
visium_heart
Spatial transcriptomics of heart tissue
Saez Lab's Repositories
saezlab/decoupleR
R package to infer biological activities from omics data using a collection of methods.
saezlab/liana-py
LIANA+: an all-in-one framework for cell-cell communication
saezlab/decoupler-py
Python package to perform enrichment analysis from omics data.
saezlab/pypath
Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.
saezlab/OmnipathR
R client for the OmniPath web service
saezlab/corneto
Unified knowledge-driven network inference from omics data
saezlab/cosmosR
COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
saezlab/omnipath
Python client for the OmniPath web service
saezlab/networkcommons
NetworkCommons is a community-driven platform designed to simplify access to tools and resources for inferring context-specific protein interaction networks by integrating context-agnostic prior knowledge with omics data.
saezlab/greta
Benchmark of GRNs using the GRETA pipeline
saezlab/MetaProViz
R-package to perform metabolomics pre-processing, differential metabolite analysis, metabolite clustering and custom visualisations.
saezlab/kasumi_bench
saezlab/FUNKI
FUNctional analysis worKflows Interface
saezlab/COSMOS_basic
tutorial to use cosmosR in the context of basic downstream analysis of differential analysis or single sample.
saezlab/GNNClinicalOutcomePrediction
saezlab/lipinet
LipiNet: A comprehensive tool for integrating and analyzing multilayer lipidomic networks. Leverage lipid interactions, pathways, and hierarchies to unlock insights into lipid metabolism and molecular functions.
saezlab/.github
saezlab/F1000_Slack
F the Bot
saezlab/MetalinksDB
saezlab/omnipath-server
The OmniPath web API
saezlab/reheat2_pub
Multicellular Transcriptional Landscape of Heart Failure
saezlab/saezlab.org-next
Playground for a new lab web site
saezlab/benchmarKIN
saezlab/cheerio
Shiny app to access cardiac hypertrophy data
saezlab/corneto-manuscript-experiments
Results using CORNETO, included in the manuscript
saezlab/CRCDiet
CRCDiet
saezlab/kidneyfibrosis_multiomicsmodel_paper
saezlab/kinase_benchmark
Comparison of different methods for kinase activity estimation
saezlab/onionnet
OnionNet
saezlab/ParTIpy
Pareto Task Inference in Python