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    258 repositories

    • decoupler-py

      Public
      Python package to perform enrichment analysis from omics data.
      pythondata-sciencebioinformaticsenrichmentnumbatranscriptomicssingle-cellenrichment-analysisspatial-transcriptomics
      Python
      •
      GNU General Public License v3.0
      •27•176•0•0•Updated Feb 5, 2025Feb 5, 2025

    • kinase_benchmark

      Public
      Comparison of different methods for kinase activity estimation
      R
      •0•0•0•0•Updated Feb 5, 2025Feb 5, 2025

    • F1000_Slack

      Public
      F the Bot
      slackbotsciwheel
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 5, 2025Feb 5, 2025

    • OmnipathR

      Public
      R client for the OmniPath web service
      proteinsnetworkspathwayscomplexesnetworks-biologyomnipathenzyme-ptm
      R
      •
      Other
      •20•125•20•0•Updated Feb 4, 2025Feb 4, 2025

    • greta

      Public
      Benchmark of GRNs using the GRETA pipeline
      Python
      •
      GNU General Public License v3.0
      •0•10•0•0•Updated Feb 4, 2025Feb 4, 2025

    • omnipath-server

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

    • MetaProViz

      Public
      R-package to perform metabolomics pre-processing, differential metabolite analysis, metabolite clustering and custom visualisations.
      HTML
      •
      GNU General Public License v3.0
      •1•13•13•0•Updated Jan 31, 2025Jan 31, 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

    • 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•10•14•1•Updated Jan 22, 2025Jan 22, 2025

    • corneto

      Public
      Unified knowledge-driven network inference from omics data
      Python
      •
      GNU General Public License v3.0
      •3•30•5•0•Updated Jan 20, 2025Jan 20, 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

    • 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
      •23•180•26•0•Updated Jan 17, 2025Jan 17, 2025

    • corneto-manuscript-experiments

      Public
      Results using CORNETO, included in the manuscript
      Jupyter Notebook
      •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

    • CRCDiet

      Public
      CRCDiet
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 9, 2025Jan 9, 2025

    • VisiumMS

      Public
      Study of Multiple Sclerosis(MS) using paried snRNA-seq and Visium transcriptmics datasets.
      Python
      •
      GNU General Public License v3.0
      •5•6•1•0•Updated Dec 11, 2024Dec 11, 2024

    • kasumi_bench

      Public
      R
      •
      GNU General Public License v3.0
      •0•5•0•0•Updated Dec 11, 2024Dec 11, 2024

    • GNNClinicalOutcomePrediction

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Dec 10, 2024Dec 10, 2024

    • benchmarKIN

      Public
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Dec 5, 2024Dec 5, 2024

    • MedInfNetworks2024

      Public
      HTML
      •0•0•0•0•Updated Dec 5, 2024Dec 5, 2024

    • saezverse

      Public
      Docker image with all tools from the lab
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

    • omnipath-metabo

      Public
      Utilities for metabolite processing
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 22, 2024Nov 22, 2024

    • 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•14•0•Updated Nov 22, 2024Nov 22, 2024

    • download-manager

      Public
      Download manager for Python
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

    • cache-manager

      Public
      A Python cache manager
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 15, 2024Nov 15, 2024

    • ocean

      Public
      R package for metabolic enzyme enrichment anaylsis
      R
      •
      GNU General Public License v3.0
      •4•11•0•0•Updated Nov 8, 2024Nov 8, 2024

    • reheat2_pub

      Public
      Multicellular Transcriptional Landscape of Heart Failure
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 7, 2024Nov 7, 2024

    • data_tools

      Public
      Collection of Python functions and classes designed to make data scientists' life easier.
      pythonsetdata-sciencedatabasemodelplot
      Python
      •
      GNU General Public License v3.0
      •5•4•0•0•Updated Oct 22, 2024Oct 22, 2024

    • 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
      •24•220•6•0•Updated Oct 19, 2024Oct 19, 2024

    • metalinks_web

      Public
      Web interface to allow contextualization of metalinksKG
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024