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/FootprintMethods_on_scRNAseq
Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data
saezlab/Omnipath_Cytoscape
a plug-in to access Omnipath from Cytoscape
saezlab/cellnopt
Tool for training of logic models of signalling networks using prior knowledge networks and perturbation data.
saezlab/Covid19
We use our tools to analysis Covid19 RNAseq datasets
saezlab/CellNOptR-MaBoSS
CellNOptR with MaBoSS simulation
saezlab/CNORode2017
modified version of CNORode including: steady state penalty, L1 regularisation, bootstrap, new transfer function
saezlab/NicheNet_Omnipath
Building and Training of the NicheNet Method exclusively using OmniPath resources. SARS-CoV-2 case study
saezlab/CARNIVAL-Bioconductor-Dev
Provisional repository for the development of CARNIVAL package for Bioconductor
saezlab/combiMS
combiMS code for Prediction of combination therapy based on perturbation modeling of the multiple sclerosis signaling network. Code started by Marti at EBI on Feb 2013
saezlab/hepatic-microenviroment
Gut microbiota fuels HCC development by shaping the hepatic inflammatory microenvironment
saezlab/network_tools
Collection of Python functions to run network-based analysis in signed and directed networks.
saezlab/NetworkModeling_course_2020
teaching materials for the network modeling course
saezlab/CRC-pathway-biomarkers
Cell-type specific parameters of signalling pathway models as biomarkers for drug sensitivity
saezlab/CXCL4_Gleitz_paper_2019
saezlab/bioconda-recipes
Conda recipes for the bioconda channel.
saezlab/CARNIVAL_cropseq
saezlab/CellNOpt-Feeder
Combining CNORFeeder with Dynamic-Feeder
saezlab/CNOv2
Main repository for the new CellNOpt features (CNOv2)
saezlab/Covid19_DrugSignatures
saezlab/Covid19_phospho
Analysis of Phosphoproteomics/Transcriptomics datasets related to SARS-CoV-2 infection
saezlab/Covid_IntestinalOrganoids
Saezlab tools on Intestinal organoids treated with Sars-CoV-2 for 60 hours
saezlab/GH_backup
Backup all repositories from a user or organization in GitHub.
saezlab/Hypertension_DAHL_rat
Pipeline scripts for analyzing the phosphoproteomic data from DAHL rat model with PHONEMeS
saezlab/KidneyMap
saezlab/LiverPeriportalization
Influence of Liver Fibrosis on Lobular Zonation
saezlab/LiverRegeneration
saezlab/ModelingMPS
code use for modeling data from Microfluidics Perturbation Screenings (MPS)
saezlab/paper_parser
Script to parse files for scientific article URLs
saezlab/prostate-phosphoSWATH_V2
Study the phospho-proteome of two prostate cancer cell lines upon perturbation with a combination of different ligands and inhibitors.
saezlab/why-pathway-methods-work