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    261 repositories

    • omnipath-server

      Public
      The OmniPath web API
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Apr 4, 2025Apr 4, 2025

    • pypath-common

      Public
      Code shared across pypath modules
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Apr 3, 2025Apr 3, 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•138•13•2•Updated Apr 3, 2025Apr 3, 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•13•12•1•Updated Apr 2, 2025Apr 2, 2025

    • kinase_benchmark

      Public
      Comparison of different methods for kinase activity estimation
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 1, 2025Apr 1, 2025

    • ParTIpy

      Public
      Pareto Task Inference in Python
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 1, 2025Apr 1, 2025

    • OmnipathR

      Public
      R client for the OmniPath web service
      proteinsnetworkspathwayscomplexesnetworks-biologyomnipathenzyme-ptm
      R
      •
      Other
      •19•131•15•0•Updated Mar 28, 2025Mar 28, 2025

    • greta

      Public
      Benchmark of GRNs using the GRETA pipeline
      Python
      •
      GNU General Public License v3.0
      •0•23•1•0•Updated Mar 22, 2025Mar 22, 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•21•14•2•Updated Mar 21, 2025Mar 21, 2025

    • kasumi_bench

      Public
      R
      •
      GNU General Public License v3.0
      •0•5•0•0•Updated Mar 21, 2025Mar 21, 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.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Mar 19, 2025Mar 19, 2025

    • reheat2_pub

      Public
      Multicellular Transcriptional Landscape of Heart Failure
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 18, 2025Mar 18, 2025

    • onionnet

      Public
      OnionNet
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 16, 2025Mar 16, 2025

    • corneto

      Public
      Unified knowledge-driven network inference from omics data
      Python
      •
      GNU General Public License v3.0
      •4•33•3•0•Updated Mar 14, 2025Mar 14, 2025

    • corneto-manuscript-experiments

      Public
      Results using CORNETO, included in the manuscript
      Jupyter Notebook
      •0•0•0•0•Updated Mar 14, 2025Mar 14, 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
      •25•235•3•0•Updated Mar 12, 2025Mar 12, 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•59•6•0•Updated Mar 9, 2025Mar 9, 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 Mar 9, 2025Mar 9, 2025

    • F1000_Slack

      Public
      F the Bot
      slackbotsciwheel
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 6, 2025Mar 6, 2025

    • kidneyfibrosis_multiomicsmodel_paper

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Mar 5, 2025Mar 5, 2025

    • omnipath

      Public
      Python client for the OmniPath web service
      Python
      •
      MIT License
      •7•44•6•0•Updated Mar 3, 2025Mar 3, 2025

    • .github

      Public
      Python
      •6•0•0•0•Updated Feb 25, 2025Feb 25, 2025

    • GNNClinicalOutcomePrediction

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Feb 14, 2025Feb 14, 2025

    • liana-py

      Public
      LIANA+: an all-in-one framework for cell-cell communication
      pythonspatialsingle-cellsingle-cell-rna-seqligand-receptorcell-cell-communicationspatialomics
      Python
      •
      GNU General Public License v3.0
      •25•200•27•0•Updated Feb 13, 2025Feb 13, 2025

    • benchmarKIN

      Public
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Feb 11, 2025Feb 11, 2025

    • decoupler-py

      Public
      Python package to perform enrichment analysis from omics data.
      pythondata-sciencebioinformaticsenrichmentnumbatranscriptomicssingle-cellenrichment-analysisspatial-transcriptomics
      Python
      •
      GNU General Public License v3.0
      •28•189•3•1•Updated Feb 7, 2025Feb 7, 2025

    • saezlab.org-next

      Public
      Playground for a new lab web site
      Astro
      •
      MIT License
      •0•0•0•0•Updated Feb 6, 2025Feb 6, 2025

    • cheerio

      Public
      Shiny app to access cardiac hypertrophy data
      R
      •0•0•0•0•Updated Jan 29, 2025Jan 29, 2025

    • MetalinksDB

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Jan 23, 2025Jan 23, 2025

    • FUNKI

      Public
      FUNctional analysis worKflows Interface
      pythonworkflowanalysisomics
      Python
      •
      GNU General Public License v3.0
      •1•4•0•0•Updated Jan 20, 2025Jan 20, 2025