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
LIANA: a LIgand-receptor ANalysis frAmework
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/cosmosR
COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
saezlab/corneto
Unified knowledge-driven network inference from omics data
saezlab/lipyd
Python module for lipidomics LC MS/MS data analysis
saezlab/flop
FunctionaL Omics Processing platform
saezlab/MetaProViz
R-package to perform metabolomics pre-processing, differential metabolite analysis, metabolite clustering and custom visualisations.
saezlab/Factor_COSMOS
Formatting NCI60 data into cosmos ready inputs and generation of testable hypothesis connecting cell-line specific TF and metabolic deregulations.
saezlab/kasumi_bench
saezlab/data_tools
Collection of Python functions and classes designed to make data scientists' life easier.
saezlab/cyrface
Bridging Cytoscape with R
saezlab/FUNKI
FUNctional analysis worKflows Interface
saezlab/cytocopter
CellNOptR in Cytoscape
saezlab/GNNClinicalOutcomePrediction
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/pypath-common
Code shared across pypath modules
saezlab/metalinks_web
Web interface to allow contextualization of metalinksKG
saezlab/omnipath-metabo
Utilities for metabolite processing
saezlab/benchmarKIN
saezlab/cache-manager
A Python cache manager
saezlab/CRCDiet
CRCDiet
saezlab/download-manager
Download manager for Python
saezlab/kidneyfibrosis_multiomicsmodel_paper
saezlab/kinase_benchmark
Comparison of different methods for kinase activity estimation
saezlab/lianaplus_manuscript
saezlab/nginx_stats
Process and visualize visitor statistics from nginx logfiles