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    283 repositories

    • liana-py

      Public
      LIANA+: an all-in-one framework for cell-cell communication
      pythonspatialsingle-cellsingle-cell-rna-seqligand-receptorcell-cell-communicationspatialomics
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •28•257•30•1•Updated Jan 8, 2026Jan 8, 2026

    • greta

      Public
      Benchmark of GRNs using the GRETA pipeline
      Python
      •
      GNU General Public License v3.0
      •2•30•5•0•Updated Jan 7, 2026Jan 7, 2026

    • pypath

      Public
      Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.
      pythondatabaseresourcenetworkmolecular-biologypathwaygenetic-regulatory-network
      Python
      •
      GNU General Public License v3.0
      •49•156•12•1•Updated Jan 6, 2026Jan 6, 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, multilayer structures, and hypergraphs.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•0•Updated Jan 2, 2026Jan 2, 2026

    • OCEAN_MCFA

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 30, 2025Dec 30, 2025

    • ParTIpy

      Public
      Pareto Task Inference in Python
      Python
      •
      GNU General Public License v3.0
      •0•8•0•1•Updated Dec 22, 2025Dec 22, 2025

    • phosphonetworks

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 22, 2025Dec 22, 2025

    • omnipath-server

      Public
      The OmniPath web API
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Dec 19, 2025Dec 19, 2025

    • organfibrosis

      Public
      A cross-organ meta-analysis of fibrotic diseases.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 18, 2025Dec 18, 2025

    • saezlab.org

      Public
      TypeScript
      •0•0•1•0•Updated Dec 18, 2025Dec 18, 2025

    • F1000_Slack

      Public
      F the Bot
      slackbotsciwheel
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Dec 17, 2025Dec 17, 2025

    • omnipath-next

      Public
      A WebApp for the Omnipath database, allowing users to browse, filter and download data.
      TypeScript
      •0•4•2•0•Updated Dec 17, 2025Dec 17, 2025

    • decoupleR

      Public
      R package to infer biological activities from omics data using a collection of methods.
      rrstatsr-package
      R
      •
      GNU General Public License v3.0
      •29•281•19•1•Updated Dec 16, 2025Dec 16, 2025

    • MetaProViz

      Public
      R-package to perform metabolomics pre-processing, differential metabolite analysis, metabolite clustering and custom visualisations.
      R
      •
      Other
      •3•16•14•1•Updated Dec 16, 2025Dec 16, 2025

    • corneto

      Public
      Unified knowledge-driven network inference from omics data
      Python
      •
      GNU General Public License v3.0
      •10•90•5•0•Updated Dec 16, 2025Dec 16, 2025

    • SpaCEy

      Public
      Jupyter Notebook
      •0•3•0•0•Updated Dec 16, 2025Dec 16, 2025

    • lipinet

      Public
      LipiNet: A comprehensive tool for integrating and analyzing multilayer lipidomic networks. Leverage lipid interactions, pathways, and hierarchies to unlock insights into lipid metabolism and molecular functions.
      Python
      •
      GNU General Public License v3.0
      •0•2•0•1•Updated Dec 14, 2025Dec 14, 2025

    • saezlab_core

      Public
      This is session handler, configuration and logging handler for Saezlab packages and applications.
      best-practicessoftware-engineering
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 12, 2025Dec 12, 2025

    • onionnet

      Public
      Fast Python toolkit (on graph-tool) for building, querying, and visualising large multi-layer graphs from DataFrames; encoding/decoding props, analysis, exports, layouts, and more.
      Python
      •
      GNU General Public License v3.0
      •1•1•0•1•Updated Dec 10, 2025Dec 10, 2025

    • CNORode

      Public
      add-on for CellNOptR using logic based differential equations
      C
      •0•3•2•0•Updated Dec 10, 2025Dec 10, 2025

    • cosmosR

      Public
      COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
      data-integrationproteomicsphosphoproteomicstranscriptomicsnetwork-modellingmetabolomic-data
      R
      •
      GNU General Public License v3.0
      •16•63•7•0•Updated Dec 10, 2025Dec 10, 2025

    • OmnipathR

      Public
      R client for the OmniPath web service
      proteinsnetworkspathwayscomplexesnetworks-biologyomnipathenzyme-ptm
      R
      •
      Other
      •21•149•19•0•Updated Dec 10, 2025Dec 10, 2025

    • ontograph

      Public
      A lightweight Python package for loading, representing, and efficiently querying biological ontologies as graph structures.
      graphsontologiesbiological-networks
      Python
      •
      MIT License
      •0•0•1•1•Updated Dec 5, 2025Dec 5, 2025

    • cache-manager

      Public
      A Python cache manager
      Python
      •
      GNU General Public License v3.0
      •0•0•2•1•Updated Dec 5, 2025Dec 5, 2025

    • python-project

      Public
      Python project template
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Dec 1, 2025Dec 1, 2025

    • PHONEMeS

      Public
      PHONEMeS (PHOsphorylation NEtworks for Mass Spectrometry) is an R package to model signalling networks based on untargeted phosphoproteomics
      R
      •
      GNU General Public License v3.0
      •5•8•0•0•Updated Nov 26, 2025Nov 26, 2025

    • CellNOptR

      Public
      Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data.
      R
      •3•13•0•1•Updated Nov 24, 2025Nov 24, 2025

    • ebi_llm_deploy_helper

      Public
      A small guide and helper to help non-technical people to deploy local LLM on EBI's HPC.
      Shell
      •0•0•0•0•Updated Nov 24, 2025Nov 24, 2025

    • download-manager

      Public
      Download manager for Python
      Python
      •
      GNU General Public License v3.0
      •0•0•2•0•Updated Nov 24, 2025Nov 24, 2025

    • ocean

      Public
      R package for metabolic enzyme enrichment anaylsis
      R
      •
      GNU General Public License v3.0
      •4•12•0•0•Updated Oct 24, 2025Oct 24, 2025