Skip to content

@microbiomedata National Microbiome Data Collaborative

Change the repository type filter

All

    Repositories list

    80 repositories

    • metadata-for-user-facility-template-transformations

      Public
      CLI tool to convert metadata submissions from the NMDC submission portal to user facility Excel templates
      Python
      •0•0•18•0•Updated Dec 24, 2024Dec 24, 2024

    • docs

      Public
      User-facing, web-based documentation about the NMDC
      documentationsphinxmkdocs
      Python
      •0•1•22•0•Updated Dec 24, 2024Dec 24, 2024

    • NMDC_documentation

      Public
      Document workflows, schemas, and portal
      3•2•19•2•Updated Dec 23, 2024Dec 23, 2024

    • nmdc-server

      Public
      Data portal client and server for NMDC.
      nmdc
      Python
      •
      Other
      •0•9•161•12•Updated Dec 23, 2024Dec 23, 2024

    • nmdc-runtime

      Public
      Runtime system for NMDC data management and orchestration
      workflownmdcmicrobiomedata
      HTML
      •
      Other
      •5•7•107•15•Updated Dec 23, 2024Dec 23, 2024

    • geoloc-tools

      Public
      Python
      •0•0•0•0•Updated Dec 23, 2024Dec 23, 2024

    • external-metadata-awareness

      Public
      Tools for fetching and processing external schemas, ontologies and metadata records. Includes value set maintenance and some GitHub org exploration.
      Jupyter Notebook
      •0•0•14•4•Updated Dec 21, 2024Dec 21, 2024

    • nmdc_automation

      Public
      Prototype automation
      Python
      •2•2•41•2•Updated Dec 20, 2024Dec 20, 2024

    • metaMS

      Public
      GC-MS Based Metabolomics Workflow
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•4•11•1•Updated Dec 20, 2024Dec 20, 2024

    • nmdc-edge

      Public
      Web-based interface to the NMDC EDGE platform
      mongoexpressnodereactjscromwell
      JavaScript
      •0•4•71•0•Updated Dec 19, 2024Dec 19, 2024

    • nmdc-schema

      Public
      National Microbiome Data Collaborative (NMDC) unified data model
      metadataschemagenomicsstandardssamplesproteomicsmetabolomicsmicrobiometranscriptomicsfair-data
      Python
      •
      Creative Commons Zero v1.0 Universal
      •8•27•363•7•Updated Dec 19, 2024Dec 19, 2024

    • nmdc_notebook_tools

      Public
      A library designed to simplify various research tasks for users looking to leverage the NMDC (National Microbiome Data Collaborative) APIs. The library provides a collection of general-purpose functions that facilitate easy access, manipulation, and analysis of microbiome data.
      Python
      •0•2•0•0•Updated Dec 19, 2024Dec 19, 2024

    • nmdc-field-notes

      Public
      Mobile app for metadata collection on the go
      reactioniccapacitor
      TypeScript
      •
      Other
      •0•1•32•0•Updated Dec 18, 2024Dec 18, 2024

    • submission-schema

      Public
      Python
      •
      MIT License
      •1•1•55•6•Updated Dec 18, 2024Dec 18, 2024

    • refscan

      Public
      Command-line program that scans NMDC database for referential integrity violations
      mongodbreferential-integritylinkml
      Python
      •0•2•4•0•Updated Dec 18, 2024Dec 18, 2024

    • mg_annotation

      Public
      Metagenome Annotation Workflow
      WDL
      •7•4•3•3•Updated Dec 18, 2024Dec 18, 2024

    • nmdc_notebooks

      Public
      Jupyter Notebooks demonstrating R and Python-based access to NMDC metadata and data
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •0•5•9•2•Updated Dec 17, 2024Dec 17, 2024

    • issues

      Public
      public repo for issues related to NMDC work
      Jupyter Notebook
      •1•2•340•1•Updated Dec 17, 2024Dec 17, 2024

    • enviroMS

      Public
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•4•3•0•Updated Dec 16, 2024Dec 16, 2024

    • metaPro

      Public
      Workflow for meta-proteomics analysis
      Python
      •
      BSD 2-Clause "Simplified" License
      •3•6•8•1•Updated Dec 15, 2024Dec 15, 2024

    • metaT_ReadCounts

      Public
      Workflow for metatranscriptome read counting
      WDL
      •0•0•0•0•Updated Dec 15, 2024Dec 15, 2024

    • metaT_Assembly

      Public
      workflow for metatranscriptome assembly
      WDL
      •0•0•1•0•Updated Dec 15, 2024Dec 15, 2024

    • metaT_ReadsQC

      Public
      Workflow for metatranscriptome quality control
      WDL
      •0•0•0•0•Updated Dec 15, 2024Dec 15, 2024

    • metaT

      Public
      Metatranscriptomics workflow
      transcriptomicsmetatranscriptomicsworkflow
      WDL
      •2•4•6•0•Updated Dec 15, 2024Dec 15, 2024

    • metaAssembly

      Public
      Workflow for metagenome assembly
      wdlwdl-workflowworkflowassemblymetagenome-assembly
      WDL
      •4•4•1•1•Updated Dec 14, 2024Dec 14, 2024

    • ReadsQC

      Public
      WDL
      •6•3•2•1•Updated Dec 14, 2024Dec 14, 2024

    • ReadbasedAnalysis

      Public
      HTML
      •6•1•0•0•Updated Dec 14, 2024Dec 14, 2024

    • metaMAGs

      Public
      Workflow for metagenome assembled genomes generation.
      Python
      •4•6•1•0•Updated Dec 14, 2024Dec 14, 2024

    • workflow_documentation

      Public
      This repository contains the documentation template for the NDMC workflows.
      Python
      •2•2•0•0•Updated Dec 5, 2024Dec 5, 2024

    • nmdc-aggregator

      Public
      Scripts that periodically aggregate data related to KEGG search
      Python
      •0•0•1•0•Updated Dec 5, 2024Dec 5, 2024