saezlab repositories

308 repositories

pypath
Public
Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular …
python database resource
python database resource network molecular-biology pathway genetic-regulatory-network
Python
•
GNU General Public License v3.0
•56•165•12•0•Updated Sep 25, 2026Sep 25, 2026
mc-astra
Public
multicellular Analysis of Sample Tissue Representations and Associations
Python
•
BSD 3-Clause "New" or "Revised" License
•2•5•0•2•Updated Sep 25, 2026Sep 25, 2026
organfibrosis
Public
A cross-organ meta-analysis of fibrotic diseases.
Python
•
GNU General Public License v3.0
•0•5•0•0•Updated Sep 24, 2026Sep 24, 2026
metabo-usecases
Public
Case studies for OmniPath Metabo manuscript
R
•
Other
•0•0•0•0•Updated Sep 24, 2026Sep 24, 2026
MetaProViz
Public
R-package to perform metabolomics pre-processing, differential metabolite analysis, metabolite clustering and custom visualisations.
R
•
Other
•4•24•15•1•Updated Sep 24, 2026Sep 24, 2026
corneto
Public
Unified knowledge-driven network inference from omics data
optimization graphs constrained-optimization
optimization graphs constrained-optimization milp omics network-analysis cvxpy biological-networks omics-data-integration
Python
•
GNU General Public License v3.0
•10•105•2•0•Updated Sep 23, 2026Sep 23, 2026
ProClaim
Public
Official code "ProClaim: Sufficiency-Aware Evidence Programming for In-the-Wild Scientific Claim Verification"
Python
•
GNU General Public License v3.0
•0•1•0•0•Updated Sep 23, 2026Sep 23, 2026
ParTIpy
Public
Pareto Task Inference in Python
Python
•
GNU General Public License v3.0
•1•23•0•1•Updated Sep 21, 2026Sep 21, 2026
modules
Public
Repository to host tool-specific module files for the Nextflow DSL2 community!
Nextflow
•
MIT License
•1.1k•0•0•0•Updated Sep 19, 2026Sep 19, 2026
heart_revremod_paper
Public
Bulk and single-nucleus RNA-seq analysis of mouse models of adverse and reverse cardiac remodeling
Jupyter Notebook
•
GNU General Public License v3.0
•0•0•0•0•Updated Sep 18, 2026Sep 18, 2026
omnipath-present
Public
Jupyter Notebook
•0•1•0•0•Updated Sep 17, 2026Sep 17, 2026
networkcommons
Public
NetworkCommons is a community-driven platform designed to simplify access to tools and resources for inferring context-specific protein interaction networks by …
Python
•
GNU General Public License v3.0
•7•34•17•3•Updated Sep 17, 2026Sep 17, 2026
omnipath-build
Public
A general database builder on top of pypath.
Jupyter Notebook
•
GNU General Public License v3.0
•0•0•0•0•Updated Sep 17, 2026Sep 17, 2026
nf-core_metaproviz
Public
R
•
GNU General Public License v3.0
•0•0•0•0•Updated Sep 15, 2026Sep 15, 2026
annnet
Public
AnnNet (Annotated Network) is a unified, high-expressivity graph platform designed to bring the convenience of AnnData-style annotated containers to networks, m…
python graph systems-biology
python graph systems-biology annotations computational-biology interoperability scientific-computing network-analysis graph-data sparse-matrix
Python
•
BSD 3-Clause "New" or "Revised" License
•0•21•0•0•Updated Sep 14, 2026Sep 14, 2026
gonads_snRNAseq_and_lipidomics_analysis_refactored
Public
Multi-omic analysis of gonadal hormone coordination in liver physiology using FCG mouse model
Jupyter Notebook
•
GNU General Public License v3.0
•0•0•0•0•Updated Sep 11, 2026Sep 11, 2026
sysbioverse
Public
Software for molecular systems biology
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Sep 11, 2026Sep 11, 2026
biology
Public
General prior knowledge integration in the Python ecosystem
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Sep 11, 2026Sep 11, 2026
saezlab.org
Public
TypeScript
•0•0•1•0•Updated Sep 10, 2026Sep 10, 2026
omnipath-metabo
Public
Compound database and metabolomics feature processing web service
Python
•
BSD 3-Clause "New" or "Revised" License
•0•1•0•0•Updated Sep 10, 2026Sep 10, 2026
omnipath-utils
Public
Prior-knowledge processing utilities Python package, database and web API
taxonomy proteins genes
taxonomy proteins genes drugs omics orthologs metabolites
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Sep 10, 2026Sep 10, 2026
OmnipathR
Public
R client for the OmniPath web service
proteins networks pathways
proteins networks pathways complexes networks-biology omnipath enzyme-ptm
R
•
Other
•25•173•22•1•Updated Sep 9, 2026Sep 9, 2026
python-project
Public
Python project template
Python
•
BSD 3-Clause "New" or "Revised" License
•2•0•0•0•Updated Sep 7, 2026Sep 7, 2026
cosmosR
Public
COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
data-integration proteomics phosphoproteomics
data-integration proteomics phosphoproteomics transcriptomics network-modelling metabolomic-data
R
•
GNU General Public License v3.0
•16•68•7•0•Updated Sep 3, 2026Sep 3, 2026
omnipath-client
Public
Python client for the new OmniPath web APIs
bioinformatics taxonomy gene-regulation
bioinformatics taxonomy gene-regulation networks metabolomics phosphoproteomics signaling transcriptomics prior-knowledge
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•1•Updated Aug 28, 2026Aug 28, 2026
kidney_biopsies_MCFA
Public
R
•
GNU General Public License v3.0
•0•0•0•0•Updated Aug 27, 2026Aug 27, 2026
CollecTRI
Public
Gene regulatory network containing signed transcription factor-target gene interactions
R
•
GNU General Public License v3.0
•9•122•0•0•Updated Aug 24, 2026Aug 24, 2026
SpaCEy
Public
Jupyter Notebook
•
GNU General Public License v3.0
•1•7•0•0•Updated Aug 23, 2026Aug 23, 2026
ontograph
Public
A lightweight Python package for loading, representing, and efficiently querying biological ontologies as graph structures.
graphs ontologies biological-networks
graphs ontologies biological-networks
Python
•
MIT License
•0•0•1•1•Updated Aug 14, 2026Aug 14, 2026
snRNASeq_Brain_Tumor_Data_Analysis
Public
Analysis of single nucleus-RNAseq Brain Dataset - Stefan Pfister
Python
•0•0•0•0•Updated Jul 22, 2026Jul 22, 2026

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Saez Lab

All

308 repositories

pypath

mc-astra

organfibrosis

metabo-usecases

MetaProViz

corneto

ProClaim

ParTIpy

modules

heart_revremod_paper

omnipath-present

networkcommons

omnipath-build

nf-core_metaproviz

annnet

gonads_snRNAseq_and_lipidomics_analysis_refactored

sysbioverse

biology

saezlab.org

omnipath-metabo

omnipath-utils

OmnipathR

python-project

cosmosR

omnipath-client

kidney_biopsies_MCFA

CollecTRI

SpaCEy

ontograph

snRNASeq_Brain_Tumor_Data_Analysis

Repositories list

308 repositories