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    297 repositories

    • gretapy

      Public
      Package to analyse and evaluate gene regulatory networks (GRNs).
      Python
      •
      MIT License
      •0•1•0•0•Updated Apr 17, 2026Apr 17, 2026

    • omnipath-metabo

      Public
      Compound database and metabolomics feature processing web service
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 17, 2026Apr 17, 2026

    • omnipath-utils

      Public
      Prior-knowledge processing utilities Python package, database and web API
      taxonomyproteinsgenes
      taxonomyproteinsgenesdrugsomicsorthologsmetabolites
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 17, 2026Apr 17, 2026

    • pypath

      Public
      Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular …
      pythondatabaseresource
      pythondatabaseresourcenetworkmolecular-biologypathwaygenetic-regulatory-network
      Python
      •
      GNU General Public License v3.0
      •49•161•11•0•Updated Apr 17, 2026Apr 17, 2026

    • F1000_Slack

      Public
      F the Bot
      slackbotsciwheel
      slackbotsciwheel
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 16, 2026Apr 16, 2026

    • MetaProViz

      Public
      R-package to perform metabolomics pre-processing, differential metabolite analysis, metabolite clustering and custom visualisations.
      R
      •
      Other
      •3•17•14•1•Updated Apr 16, 2026Apr 16, 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…
      pythongraphsystems-biology
      pythongraphsystems-biologyannotationscomputational-biologyinteroperabilityscientific-computingnetwork-analysisgraph-datasparse-matrix
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•9•0•0•Updated Apr 14, 2026Apr 14, 2026

    • ParTIpy

      Public
      Pareto Task Inference in Python
      Python
      •
      GNU General Public License v3.0
      •0•11•0•0•Updated Apr 13, 2026Apr 13, 2026

    • OmnipathR

      Public
      R client for the OmniPath web service
      proteinsnetworkspathways
      proteinsnetworkspathwayscomplexesnetworks-biologyomnipathenzyme-ptm
      R
      •
      Other
      •21•164•21•0•Updated Apr 13, 2026Apr 13, 2026

    • saezlab.org

      Public
      TypeScript
      •0•0•1•0•Updated Apr 10, 2026Apr 10, 2026

    • omnipath-client

      Public
      The new implementation for the OmniPath Python client
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•1•Updated Apr 9, 2026Apr 9, 2026

    • dlmachine

      Public
      Download manager for Python
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 9, 2026Apr 9, 2026

    • cachedir

      Public
      A Python cache manager
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 9, 2026Apr 9, 2026

    • pkg-infra

      Public
      Session, config and log handler for Saezlab Python packages
      best-practicessoftware-engineering
      best-practicessoftware-engineering
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 5, 2026Apr 5, 2026

    • MINA

      Public
      Multicellular INtegration Analysis
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Apr 1, 2026Apr 1, 2026

    • python-project

      Public
      Python project template
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Mar 31, 2026Mar 31, 2026

    • SpaCEy

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•6•0•0•Updated Mar 25, 2026Mar 25, 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 Mar 24, 2026Mar 24, 2026

    • CRCDiet

      Public
      CRCDiet
      Python
      •
      MIT License
      •0•1•0•0•Updated Mar 24, 2026Mar 24, 2026

    • greta

      Public
      Benchmark of GRNs using the GRETA pipeline
      Python
      •
      GNU General Public License v3.0
      •3•31•5•0•Updated Mar 18, 2026Mar 18, 2026

    • cosmosR

      Public
      COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
      data-integrationproteomicsphosphoproteomics
      data-integrationproteomicsphosphoproteomicstranscriptomicsnetwork-modellingmetabolomic-data
      R
      •
      GNU General Public License v3.0
      •16•69•7•0•Updated Mar 17, 2026Mar 17, 2026

    • organfibrosis

      Public
      A cross-organ meta-analysis of fibrotic diseases.
      Python
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Mar 12, 2026Mar 12, 2026

    • ontograph

      Public
      A lightweight Python package for loading, representing, and efficiently querying biological ontologies as graph structures.
      graphsontologiesbiological-networks
      graphsontologiesbiological-networks
      Python
      •
      MIT License
      •0•0•1•1•Updated Mar 10, 2026Mar 10, 2026

    • multiomics2026

      Public
      EBI multiomics training CORNETO project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•0•Updated Mar 6, 2026Mar 6, 2026

    • corneto-ebi-multiomics

      Public
      A project for the EBI multiomics training
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Mar 5, 2026Mar 5, 2026

    • omnipath-server

      Public
      The OmniPath web API
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Mar 3, 2026Mar 3, 2026

    • Omnipath_Cytoscape

      Public
      a plug-in to access Omnipath from Cytoscape
      Java
      •
      GNU General Public License v3.0
      •0•8•2•0•Updated Mar 3, 2026Mar 3, 2026

    • COSMOS_basic

      Public
      tutorial to use cosmosR in the context of basic downstream analysis of differential analysis or single sample.
      R
      •
      GNU General Public License v3.0
      •0•2•1•0•Updated Mar 3, 2026Mar 3, 2026

    • teaching_material

      Public
      teaching material for various courses
      courseteaching-materials
      courseteaching-materials
      HTML
      •
      GNU General Public License v3.0
      •3•2•0•0•Updated Feb 27, 2026Feb 27, 2026

    • corneto

      Public
      Unified knowledge-driven network inference from omics data
      biologyoptimizationgraphs
      biologyoptimizationgraphsconstrained-optimizationomicsnetwork-analysiscvxpybiological-networksomics-data-integrationcausal-discovery
      Python
      •
      GNU General Public License v3.0
      •10•99•3•0•Updated Feb 27, 2026Feb 27, 2026
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