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    272 repositories

    • ParTIpy_paper

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Aug 1, 2025Aug 1, 2025

    • onionnet

      Public
      OnionNet
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 1, 2025Aug 1, 2025

    • omnipath-next

      Public
      A WebApp for the Omnipath database, allowing users to browse, filter and download data.
      TypeScript
      •0•0•0•0•Updated Aug 1, 2025Aug 1, 2025

    • MetaProViz

      Public
      R-package to perform metabolomics pre-processing, differential metabolite analysis, metabolite clustering and custom visualisations.
      R
      •
      GNU General Public License v3.0
      •3•15•13•1•Updated Aug 1, 2025Aug 1, 2025

    • greta

      Public
      Benchmark of GRNs using the GRETA pipeline
      Python
      •
      GNU General Public License v3.0
      •1•26•4•0•Updated Jul 31, 2025Jul 31, 2025

    • corneto

      Public
      Unified knowledge-driven network inference from omics data
      Python
      •
      GNU General Public License v3.0
      •7•65•7•0•Updated Jul 29, 2025Jul 29, 2025

    • corneto-data

      Public
      Repository with data and resources that can be accessed through CORNETO's API
      Python
      •0•0•0•0•Updated Jul 29, 2025Jul 29, 2025

    • pypath

      Public
      Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.
      databaseresourcenetworkmolecular-biologypathwaygenetic-regulatory-networkpython
      Python
      •
      GNU General Public License v3.0
      •48•147•11•0•Updated Jul 28, 2025Jul 28, 2025

    • ParTIpy

      Public
      Pareto Task Inference in Python
      Python
      •
      GNU General Public License v3.0
      •0•0•0•1•Updated Jul 28, 2025Jul 28, 2025

    • saezlab.org

      Public
      TypeScript
      •0•0•1•0•Updated Jul 28, 2025Jul 28, 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•2•Updated Jul 28, 2025Jul 28, 2025

    • FUNKI

      Public
      FUNctional analysis worKflows Interface
      pythonworkflowanalysisomics
      Python
      •
      GNU General Public License v3.0
      •1•4•0•0•Updated Jul 23, 2025Jul 23, 2025

    • omnipath-metabo

      Public
      Utilities for metabolite processing
      Python
      •
      GNU General Public License v3.0
      •1•0•1•0•Updated Jul 23, 2025Jul 23, 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•1•0•0•Updated Jul 23, 2025Jul 23, 2025

    • networkcommons

      Public
      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.
      Python
      •
      GNU General Public License v3.0
      •4•25•17•2•Updated Jul 23, 2025Jul 23, 2025

    • scDoRI_greta

      Public
      scDoRI (single-cell Deep multi-Omic Regulatory Inference) is a deep learning model to infer enhancer-mediated gene regulatory networks (eGRNs) from single-cell multiome data (RNA + ATAC). Implementation for GRETA pipeline
      Python
      •
      MIT License
      •4•0•0•0•Updated Jul 18, 2025Jul 18, 2025

    • MultispectralHCC

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 16, 2025Jul 16, 2025

    • OmnipathR

      Public
      R client for the OmniPath web service
      proteinsnetworkspathwayscomplexesnetworks-biologyomnipathenzyme-ptm
      R
      •
      Other
      •20•137•16•0•Updated Jul 16, 2025Jul 16, 2025

    • 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
      •27•223•37•0•Updated Jul 14, 2025Jul 14, 2025

    • incura_app

      Public
      Code for Streamlit application of incur
      Python
      •
      Creative Commons Zero v1.0 Universal
      •1•0•0•0•Updated Jul 11, 2025Jul 11, 2025

    • QC_MALDIMSI

      Public
      Quality Control for MALDI-MSI
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 6, 2025Jul 6, 2025

    • 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•1•1•0•Updated Jul 6, 2025Jul 6, 2025

    • cosmosR

      Public
      COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
      data-integrationproteomicsphosphoproteomicsnetwork-modellingtranscriptomicsmetabolomic-data
      R
      •
      GNU General Public License v3.0
      •16•62•7•0•Updated Jul 6, 2025Jul 6, 2025

    • incura

      Public
      Python
      •1•0•0•0•Updated Jun 27, 2025Jun 27, 2025

    • omnipath

      Public
      Python client for the OmniPath web service
      Python
      •
      MIT License
      •9•45•7•0•Updated Jun 26, 2025Jun 26, 2025

    • reheat2_pub

      Public
      Multicellular Transcriptional Landscape of Heart Failure
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•1•0•Updated Jun 13, 2025Jun 13, 2025

    • reheat2_shiny

      Public
      shiny app to access results from ReHeaT2
      HTML
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 12, 2025Jun 12, 2025

    • saezlab-resources-hub

      Public
      Kickstart your Software Engineering journey with this comprehensive resource hub, curated by the Saez-Rodriguez Group to support learning, best practices, and hands-on development.
      bioinformaticsbest-practicessoftware-engineering
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 11, 2025Jun 11, 2025

    • python-project

      Public
      Python project template
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•1•Updated Jun 11, 2025Jun 11, 2025

    • omnipath-server

      Public
      The OmniPath web API
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jun 6, 2025Jun 6, 2025