Data

Tools

Indexes

Applications

Experiments

Awesome

An open API service indexing awesome lists of open source software.

Projects in Awesome Lists by saezlab

A curated list of projects in awesome lists by saezlab .

https://github.com/saezlab/decoupler

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

r r-package rstats

Last synced: 10 Apr 2025

https://github.com/saezlab/decoupleR

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

r r-package rstats

Last synced: 07 Oct 2025

https://github.com/saezlab/liana

LIANA: a LIgand-receptor ANalysis frAmework

cell-cell-communication cellchat cellphonedb liana ligand-receptor omnipath

Last synced: 07 Apr 2025

https://github.com/saezlab/liana-py

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

cell-cell-communication ligand-receptor python single-cell single-cell-rna-seq spatial spatialomics

Last synced: 05 Apr 2025

https://github.com/saezlab/pypath

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

database genetic-regulatory-network molecular-biology network pathway python resource

Last synced: 12 Apr 2025

https://github.com/saezlab/omnipathr

R client for the OmniPath web service

complexes enzyme-ptm networks networks-biology omnipath pathways proteins

Last synced: 05 Apr 2025

https://github.com/saezlab/OmnipathR

R client for the OmniPath web service

complexes enzyme-ptm networks networks-biology omnipath pathways proteins

Last synced: 18 Jul 2025

https://github.com/saezlab/progeny

R package for Pathway RespOnsive GENe activity inference

Last synced: 06 Apr 2025

https://github.com/saezlab/corneto

Unified knowledge-driven network inference from omics data

Last synced: 07 Feb 2026

https://github.com/saezlab/visium_heart

Spatial transcriptomics of heart tissue

Last synced: 14 Apr 2025

https://github.com/saezlab/collectri

Gene regulatory network containing signed transcription factor-target gene interactions

Last synced: 14 Apr 2025

https://github.com/saezlab/cosmosr

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

data-integration metabolomic-data network-modelling phosphoproteomics proteomics transcriptomics

Last synced: 09 Apr 2025

https://github.com/saezlab/carnival

CAusal Reasoning for Network Identification with integer VALue programming in R

causal-models footprints integer-linear-programming pathway-enrichment-analysis r

Last synced: 13 Oct 2025

https://github.com/saezlab/transcriptutorial

This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL

Last synced: 16 Mar 2026

https://github.com/saezlab/omnipath

Python client for the OmniPath web service

Last synced: 05 Apr 2025

https://github.com/saezlab/footprintmethods_on_scrnaseq

Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data

Last synced: 12 Sep 2025

https://github.com/saezlab/greta

Benchmark of GRNs using the GRETA pipeline

Last synced: 02 Jul 2025

https://github.com/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.

Last synced: 14 Apr 2025

https://github.com/saezlab/footprints

Analysis code for "Perturbation-response genes reveal signaling footprints in cancer gene expression"

Last synced: 13 Jul 2025

https://github.com/saezlab/metaproviz

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

Last synced: 30 Jan 2026

https://github.com/saezlab/lipyd

Python module for lipidomics LC MS/MS data analysis

lc-msms lipidomics openms python

Last synced: 17 Jun 2025

https://github.com/saezlab/flop

FunctionaL Omics Processing platform

Last synced: 14 Apr 2025

https://github.com/saezlab/shinyfunki

FUNctional toolKIt platform for multi-omic functional analysis. An standardised pipeline to analysis transcriptomic, proteomic, phosphoproteomic and metabolomic datasets.

carnival cosmos dorothea footprint-analysis progeny shiny-apps

Last synced: 14 Apr 2025

https://github.com/saezlab/ocean

R package for metabolic enzyme enrichment anaylsis

Last synced: 14 Apr 2025

https://github.com/saezlab/mofacell

Code used for muti cellular factor analysis

Last synced: 14 Apr 2025

https://github.com/saezlab/progeny-py

PROGENY Python implementation

Last synced: 14 Apr 2025

https://github.com/saezlab/cellnoptr

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

Last synced: 14 Apr 2025

https://github.com/saezlab/dorothea-py

Dorothea package in Python

Last synced: 09 Jul 2025

https://github.com/saezlab/kinact

Toolbox for Kinase Activity Scoring based on phosphoproteomic data

Last synced: 14 Apr 2025

https://github.com/saezlab/decoupler_manuscript

Code to reproduce the results from decoupleR's manuscript

Last synced: 07 Oct 2025

https://github.com/saezlab/slapenrich

Sample Level Analysis of Pathway Alteration Enrichments

Last synced: 02 Apr 2026

https://github.com/saezlab/mofacellular

R package to infer multicellular programs from single-cell data using multi-omics factor analysis (MOFA)

Last synced: 14 Apr 2025

https://github.com/saezlab/factor_cosmos

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

Last synced: 02 Jan 2026

https://github.com/saezlab/decouplerbench

Package to benchmark methods from decoupleR

Last synced: 14 Apr 2025

https://github.com/saezlab/visiumms

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

Last synced: 14 Apr 2025

https://github.com/saezlab/eccb2022_sc_funcomics

Functional analysis of single-cell transcriptomics

Last synced: 02 Jan 2026

https://github.com/saezlab/omnipath_cytoscape

a plug-in to access Omnipath from Cytoscape

Last synced: 11 Jul 2025

https://github.com/saezlab/phonemes

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

Last synced: 14 Apr 2025

https://github.com/saezlab/scell_hfpef

single cell RNAseq analysis of HFpEF mice model

Last synced: 28 Jun 2025

https://github.com/saezlab/ligrec_decouple

Systematic Comparison of Cell-Cell Communication Tools and Resources

Last synced: 14 Apr 2025

https://github.com/saezlab/hf_meta-analysis

Code that generates results and figures from: "A Consensus Transcriptional Landscape of Human End-Stage Heart Failure"

Last synced: 14 Apr 2025

https://github.com/saezlab/permedcoe_summer_school_2023

PerMedCoE summer school 2023

Last synced: 14 Apr 2025

https://github.com/saezlab/funki

FUNctional analysis worKflows Interface

analysis omics python workflow

Last synced: 14 Apr 2025

https://github.com/saezlab/cellnopt

Tool for training of logic models of signalling networks using prior knowledge networks and perturbation data.

Last synced: 01 Jan 2026

https://github.com/saezlab/covid19

We use our tools to analysis Covid19 RNAseq datasets

Last synced: 01 Jan 2026

https://github.com/saezlab/visium_colon_si

ST pipelines on mouse colon and small intestine

Last synced: 04 Aug 2025

https://github.com/saezlab/cpt_qsptutorial

Supplementary material for CPT tutorial on logic modeling for quantitative systems pharmacology

Last synced: 14 Apr 2025

https://github.com/saezlab/kinase_tf_mini_tuto

This is a short tutorial to show in parallel how to estimate TF and kinase activities from transcriptomic and phosphoproteomic data

Last synced: 14 Apr 2025

https://github.com/saezlab/protein_attenuation

Proteogenomics analsysis of protein attenuation in tumours

Last synced: 06 Oct 2025

https://github.com/saezlab/cnorode

add-on for CellNOptR using logic based differential equations

Last synced: 06 Oct 2025

https://github.com/saezlab/liverx

Analysis of liver proteomics data from Aebersold lab

Last synced: 10 Feb 2026

https://github.com/saezlab/cyrface

Bridging Cytoscape with R

Last synced: 26 Oct 2025

https://github.com/saezlab/teaching_material

teaching material for various courses

course teaching-materials

Last synced: 03 Jan 2026

https://github.com/saezlab/shinycnor

Shiny application for the CellNOptR packages

Last synced: 22 Aug 2025

https://github.com/saezlab/nichenet_omnipath

Building and Training of the NicheNet Method exclusively using OmniPath resources. SARS-CoV-2 case study

Last synced: 02 Jan 2026

https://github.com/saezlab/conservedfootprints

Transfer of regulatory knowledge from human to mouse for functional genomics analysis

Last synced: 15 Mar 2025

https://github.com/saezlab/bradiplus

BraDiPluS (Braille Display Plugs Data Analysis) is an R package to process and analyse data produced using the microfluidic platform for functional drug screening of patient biopsies developed in collaboration with Merten group (EMBL).

Last synced: 25 Aug 2025

https://github.com/saezlab/2024_ebi_grn

Materials for the 2024 course at EMBL-EBI: "Modelling gene regulation from transcriptomics and chromatin accessibility single-cell data".

Last synced: 15 Mar 2025

https://github.com/saezlab/tumordeconvolution

Estimate tumor purities from gene expression data

Last synced: 31 Jan 2026

https://github.com/saezlab/cytocopter

CellNOptR in Cytoscape

Last synced: 02 Apr 2026

https://github.com/saezlab/process_rnaseq_cellines

Processing RNAseq data from Cell Lines. From raw data to normalised, voom and ComBat batch-correction

Last synced: 03 Jul 2026

https://github.com/saezlab/cnorode2017

modified version of CNORode including: steady state penalty, L1 regularisation, bootstrap, new transfer function

Last synced: 08 Oct 2025

https://github.com/saezlab/singlecell_course_2022

Teaching material for the single-cell course 2022

Last synced: 02 Jan 2026

https://github.com/saezlab/permedcoe_tools_virtual_course_2023

Material for the PerMedCoE virtual course: transcriptomics to mechanistic models of signalling.

Last synced: 14 Apr 2025

https://github.com/saezlab/scheduling

Repository to collect issues for events to be scheduled

Last synced: 15 Mar 2025

https://github.com/saezlab/cellnoptr-maboss

CellNOptR with MaBoSS simulation

Last synced: 15 Mar 2025

https://github.com/saezlab/tfbenchmark

This repository contains the code used to benchmark TF-target datasets via TF activities in 3 benchmark datasets

benchmark datasets regulons

Last synced: 19 Jul 2025

https://github.com/saezlab/neo4j-utils

Rich interface on top of the official Neo4j driver

Last synced: 07 Jul 2025

https://github.com/saezlab/microbiome_analysis_course_2022

Mobi microbiome course materials

Last synced: 02 Jan 2026

https://github.com/saezlab/carnival-bioconductor-dev

Provisional repository for the development of CARNIVAL package for Bioconductor

Last synced: 05 Oct 2025

https://github.com/saezlab/phonemes-ilp

ILP implementation of PHONEMeS

Last synced: 15 Mar 2025

https://github.com/saezlab/uptown

Last synced: 15 Mar 2025

https://github.com/saezlab/macau_synergy_prediction

Target functional similarity based workflows for drug synergy prediction and stratification

Last synced: 13 Jun 2025

https://github.com/saezlab/xu_tubuloid

Last synced: 03 Jan 2026

https://github.com/saezlab/network_tools

Collection of Python functions to run network-based analysis in signed and directed networks.

igraph networks networks-biology networkx python3 r

Last synced: 12 May 2026

https://github.com/saezlab/liver-disease-atlas

Transcriptomic cross-species analysis of chronic liver disease reveals consistent regulation between humans and mice

bioinformatics liver-disease meta-analysis transcriptomics workflowr

Last synced: 15 Mar 2025

https://github.com/saezlab/omnipath_analysis

analysis and visualization workflows for the OmniPath 2 paper

Last synced: 16 Aug 2025

https://github.com/saezlab/gene-network-inference-in-r

Mutual information-based and bicor-based methods for genome-wide reverse engineering of gene regulatory networks in R.

Last synced: 02 Jan 2026

https://github.com/saezlab/yeast_phospho

Systematic analysis of transcriptional and post-transcriptional regulation of metabolism in yeast

Last synced: 06 Jul 2026

https://github.com/saezlab/oncosignature

Scripts used to perform the analyses of OncoSignature project for AML

Last synced: 30 Jul 2025

https://github.com/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

Last synced: 15 Mar 2025

https://github.com/saezlab/insilico_tissue_simulator

simulator used for the Misty paper

Last synced: 15 Mar 2025

https://github.com/saezlab/cosmos-tpp

repository to summarise COSMOS-TPP work

Last synced: 15 Mar 2025

https://github.com/saezlab/cnorfeeder

CellNOptR add-on that permits to extend a network with links derived from literature

Last synced: 20 Sep 2025

https://github.com/saezlab/cosmos_meta_pkn_redhuman

new lighter and streamlined PKN generation, based on redHuman reaction network

Last synced: 27 Jul 2025