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    379 repositories

    • archs4dx

      Public
      JavaScript
      •
      Apache License 2.0
      •0•0•2•0•Updated Mar 28, 2025Mar 28, 2025

    • CoauthorshipNetworkDemo

      Public
      KnowledgeGraph Demo
      Jupyter Notebook
      •12•0•0•0•Updated Mar 28, 2025Mar 28, 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
      •13•0•0•0•Updated Mar 27, 2025Mar 27, 2025

    • CFDECoauthorNetwork

      Public
      A fork to create the CFDECoauthorNetwork.
      JavaScript
      •
      Other
      •13•0•6•0•Updated Mar 26, 2025Mar 26, 2025

    • hypothesispage

      Public
      Simple hypothesis page, much simpler just to show PrismExp results
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 26, 2025Mar 26, 2025

    • DRC-Portals

      Public
      TypeScript
      •0•0•31•7•Updated Mar 25, 2025Mar 25, 2025

    • drc-static

      Public
      Jupyter Notebook
      •0•0•0•1•Updated Mar 25, 2025Mar 25, 2025

    • blitzgsea

      Public
      Fast Gene Set Enrichment Analysis (GSEA) implementation of the prerank algorithm. Use Loess interpolation of bimodal ES distribution for accurate p-value estimation.
      Jupyter Notebook
      •
      Apache License 2.0
      •9•46•0•0•Updated Mar 24, 2025Mar 24, 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
      •18•11•39•0•Updated Mar 24, 2025Mar 24, 2025

    • archs4r

      Public
      R package to load and query ARCHS4 data in R
      R
      •
      Apache License 2.0
      •0•2•0•0•Updated Mar 21, 2025Mar 21, 2025

    • ufs

      Public
      Python Universal File System (UFS)
      Python
      •0•0•0•0•Updated Mar 20, 2025Mar 20, 2025

    • flaskmakerai

      Public
      AI do develop and deploy flask apps
      HTML
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 19, 2025Mar 19, 2025

    • archs4py

      Public
      Python package to load and query ARCHS4 data
      Python
      •
      Apache License 2.0
      •3•19•2•0•Updated Mar 12, 2025Mar 12, 2025

    • Enrichr-Viz-Appyter

      Public
      Appyter for enrichr canvases, scatter plots, and Manhattan plots
      Jupyter Notebook
      •2•0•3•0•Updated Mar 11, 2025Mar 11, 2025

    • speedrichr

      Public
      Java
      •2•0•0•0•Updated Mar 11, 2025Mar 11, 2025

    • HarmonizomePythonScripts

      Public
      Jupyter Notebook
      •10•23•0•1•Updated Mar 10, 2025Mar 10, 2025

    • ChEA-KG

      Public
      Demo of how to build a transcription factor KG using the KG UI
      Jupyter Notebook
      •12•0•0•0•Updated Mar 10, 2025Mar 10, 2025

    • datacrosswaysarchs4

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 6, 2025Mar 6, 2025

    • sigcom-lincs

      Public
      Signature Commons LINCS Repo
      HTML
      •3•3•9•0•Updated Feb 24, 2025Feb 24, 2025

    • server-templates

      Public
      Docker containers of preconfigured servers and web application stacks.
      TypeScript
      •3•3•0•0•Updated Feb 24, 2025Feb 24, 2025

    • 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.
      neo4jneo4j-databaseknowledge-graphcytoscapenetworksuser-interfacegeneset-enrichmentcytoscapejscypher-query-languagenetworkscience
      JavaScript
      •
      Other
      •13•8•5•1•Updated Feb 20, 2025Feb 20, 2025

    • dokku

      Public
      Ma'ayanlab dokku server admin and user guide
      Shell
      •
      Other
      •0•2•0•1•Updated Feb 14, 2025Feb 14, 2025

    • GeneSetCart

      Public
      GeneSetCart is an interactive web-based platform that enables investigators to gather gene sets from various sources; augment these sets with gene-gene co-expression correlations and protein-protein interactions; perform set operations on these sets such as union, consensus, and intersection; and visualize and analyze these gene sets.
      genomicsbiomedical-informaticsproteomicstranscriptomicsgeneset-enrichmentbiomedical-data-sciencegenesetsgeneset-enrichment-analysisproteomics-data-analysis
      TypeScript
      •
      GNU General Public License v3.0
      •0•0•4•0•Updated Feb 10, 2025Feb 10, 2025

    • RummageneXRummaGEO

      Public
      Jupyter Notebook
      •0•0•2•0•Updated Jan 24, 2025Jan 24, 2025

    • KnowledgeGraphUIDemo

      Public
      KnowledgeGraph Demo
      Jupyter Notebook
      •12•1•0•0•Updated Jan 23, 2025Jan 23, 2025

    • prismexp

      Public
      Advanced gene function prediction
      Python
      •
      Apache License 2.0
      •0•7•2•0•Updated Jan 22, 2025Jan 22, 2025

    • GenesToWordCloud

      Public
      Remake of Genes2WordCloud
      JavaScript
      •0•0•0•0•Updated Jan 15, 2025Jan 15, 2025

    • rummagene

      Public
      Python
      •
      Other
      •3•9•7•0•Updated Dec 18, 2024Dec 18, 2024

    • EnrichrPythonScripts

      Public
      Python Jupyter notebooks for Enrichr species databases
      Jupyter Notebook
      •0•3•0•0•Updated Dec 11, 2024Dec 11, 2024

    • rummageo

      Public
      Jupyter Notebook
      •
      Other
      •3•2•1•0•Updated Dec 11, 2024Dec 11, 2024