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    387 repositories

    • Knowledge-Graph-UI

      Public
      Knowledge-Graph-UI (KG-UI) is an open-source web-based user interface built for KGs stored in Neo4j. The UI features Cypher queries for viewing immediate neighbors as well as shortest paths between two entities. Additionally, the API can be extended to add other functions such as enrichment analysis, and specialized queries. Example implementation:
      neo4jneo4j-databaseknowledge-graphcytoscapenetworksuser-interfacegeneset-enrichmentcytoscapejscypher-query-languagenetworkscience
      TypeScript
      •
      Other
      •18•17•5•1•Updated Dec 2, 2025Dec 2, 2025

    • appyter

      Public
      jinja2-enabled jupyter notebooks
      Python
      •
      Other
      •6•37•15•9•Updated Dec 2, 2025Dec 2, 2025

    • DRC-Portals

      Public
      This repo has the code for the CFDE Workbench. The workbench serves the CFDE Information Portal and the CFDE Data Portal
      ot2od036435
      TypeScript
      •0•0•20•2•Updated Nov 21, 2025Nov 21, 2025

    • sc2DAT

      Public
      JavaScript
      •0•1•2•0•Updated Nov 21, 2025Nov 21, 2025

    • datadistillery-kg

      Public
      Jupyter Notebook
      •0•0•4•0•Updated Nov 18, 2025Nov 18, 2025

    • Enrichr-Viz-Appyter

      Public
      Appyter for enrichr canvases, scatter plots, and Manhattan plots
      Jupyter Notebook
      •2•0•3•0•Updated Nov 14, 2025Nov 14, 2025

    • proxy

      Public
      A convenient and generic proxy image
      Shell
      •
      Apache License 2.0
      •1•0•0•0•Updated Oct 31, 2025Oct 31, 2025

    • ChEA-KG-UI

      Public
      Knowledge-Graph-UI (KG-UI) is an open-source web-based user interface built for KGs stored in Neo4j. The UI features Cypher queries for viewing immediate neighbors as well as shortest paths between two entities. Additionally, the API can be extended to add other functions such as enrichment analysis, and specialized queries.
      TypeScript
      •
      GNU General Public License v3.0
      •18•0•0•0•Updated Oct 28, 2025Oct 28, 2025

    • mcp-template

      Public
      template for mcp server using the typescript sdk
      TypeScript
      •0•0•0•0•Updated Oct 27, 2025Oct 27, 2025

    • cfde-c2m2

      Public
      A collection of utilities for simplifying the C2M2 submission process.
      Python
      •0•2•0•0•Updated Oct 22, 2025Oct 22, 2025

    • cfde-wheel

      Public
      Documentation for CFDE Navigation Wheel
      TypeScript
      •
      Other
      •1•1•0•1•Updated Oct 21, 2025Oct 21, 2025

    • drc-static

      Public
      Jupyter Notebook
      •0•0•0•1•Updated Oct 21, 2025Oct 21, 2025

    • Playbook-Workflow-Builder

      Public
      A repository for the Playbook Workflow Builder project.
      workflowdata-sciencebioinformaticsgene-setsbiologysystems-biologygene-expressiongene-ontologyproteomicscwl
      TypeScript
      •
      Creative Commons Attribution 4.0 International
      •19•23•40•0•Updated Oct 20, 2025Oct 20, 2025

    • EnrichrPythonScripts

      Public
      Python Jupyter notebooks for Enrichr species databases
      Jupyter Notebook
      •0•3•0•0•Updated Oct 8, 2025Oct 8, 2025

    • appyter-catalog

      Public
      A catalog of appyter notebooks
      Jupyter Notebook
      •
      Other
      •48•40•25•5•Updated Oct 7, 2025Oct 7, 2025

    • gsfm-predictions

      Public
      TypeScript
      •0•0•1•0•Updated Oct 6, 2025Oct 6, 2025

    • rummagene

      Public
      Python
      •
      Other
      •3•12•7•0•Updated Sep 30, 2025Sep 30, 2025

    • gsfm

      Public
      The gene set foundation model training, evaluation, and benchmark code.
      Jupyter Notebook
      •0•0•0•0•Updated Sep 26, 2025Sep 26, 2025

    • c2m2-assessment

      Public
      This application may be used for performing assessments on C2M2 datapackages
      Python
      •1•0•0•0•Updated Sep 19, 2025Sep 19, 2025

    • postgrest-drs

      Public
      A PostgREST powered DRS server
      PLpgSQL
      •
      Other
      •0•0•0•0•Updated Sep 18, 2025Sep 18, 2025

    • FAIRshake

      Public
      HTML
      •
      Other
      •6•10•28•6•Updated Aug 28, 2025Aug 28, 2025

    • xalign

      Public
      Hassle-free RNA-seq alignment
      Python
      •
      Apache License 2.0
      •1•0•0•0•Updated Aug 7, 2025Aug 7, 2025

    • KEA-KG-UI

      Public
      Knowledge-Graph-UI (KG-UI) is an open-source web-based user interface built for KGs stored in Neo4j. The UI features Cypher queries for viewing immediate neighbors as well as shortest paths between two entities. Additionally, the API can be extended to add other functions such as enrichment analysis, and specialized queries.
      TypeScript
      •
      GNU General Public License v3.0
      •18•0•0•0•Updated Aug 6, 2025Aug 6, 2025

    • k8s-docs

      Public
      Ma'ayanlab k8s server admin and user guide
      Python
      •
      Other
      •1•0•0•0•Updated Jul 30, 2025Jul 30, 2025

    • archs4dx

      Public
      JavaScript
      •
      Apache License 2.0
      •0•1•6•0•Updated Jul 30, 2025Jul 30, 2025

    • server-templates

      Public
      Docker containers of preconfigured servers and web application stacks.
      TypeScript
      •4•4•0•0•Updated Jul 30, 2025Jul 30, 2025

    • archs4py

      Public
      Python package to load and query ARCHS4 data
      Python
      •
      Apache License 2.0
      •3•24•3•0•Updated Jul 25, 2025Jul 25, 2025

    • KnowledgeGraphUIDemo

      Public
      KnowledgeGraph Demo
      Jupyter Notebook
      •13•2•0•0•Updated Jul 25, 2025Jul 25, 2025

    • PINetworkDemo

      Public
      KnowledgeGraph Demo
      Jupyter Notebook
      •13•0•0•0•Updated Jul 20, 2025Jul 20, 2025

    • biojupies-plugins

      Public
      User-submitted RNA-seq data analysis tools for BioJupies.
      bioinformaticsjupytersystems-biology
      Python
      •
      Apache License 2.0
      •13•20•12•1•Updated Jul 16, 2025Jul 16, 2025