Pinned Repositories
berkeley-schema-fy24
A fork of the nmdc-schema, for refactoring based on Monterey insights
metaMAGs
Workflow for metagenome assembled genomes generation.
metaPro
Workflow for meta-proteomics analysis
mixs-6-2-release-candidate
Proposed, Harmonized MIxS 6.2
nmdc-schema
National Microbiome Data Collaborative (NMDC) unified data model
nmdc-server
Data portal client and server for NMDC.
NMDC_documentation
Document workflows, schemas, and portal
nmdc_notebooks
Jupyter Notebooks demonstrating R and Python-based access to NMDC metadata and data
sample-annotator
NMDC Sample Annotator
WorkflowPlanning
This is primarily a repo for capturing policies and discussions around the different workflows for NMDC. This is also used for project management related pieces.
National Microbiome Data Collaborative's Repositories
microbiomedata/nmdc-schema
National Microbiome Data Collaborative (NMDC) unified data model
microbiomedata/nmdc-server
Data portal client and server for NMDC.
microbiomedata/berkeley-schema-fy24
A fork of the nmdc-schema, for refactoring based on Monterey insights
microbiomedata/metaMAGs
Workflow for metagenome assembled genomes generation.
microbiomedata/nmdc_notebooks
Jupyter Notebooks demonstrating R and Python-based access to NMDC metadata and data
microbiomedata/enviroMS
microbiomedata/metaAssembly
Workflow for metagenome assembly
microbiomedata/metaMS
GC-MS Based Metabolomics Workflow
microbiomedata/metaT
Metatranscriptomics workflow
microbiomedata/nmdc-runtime
Runtime system for NMDC data management and orchestration
microbiomedata/mg_annotation
Metagenome Annotation Workflow
microbiomedata/nmdc-edge
Web-based interface to the NMDC EDGE platform
microbiomedata/ReadsQC
microbiomedata/nmdc_automation
Prototype automation
microbiomedata/NMDC_documentation
Document workflows, schemas, and portal
microbiomedata/workflow_documentation
This repository contains the documentation template for the NDMC workflows.
microbiomedata/DataHarmonizer
Our dev interface is available via github pages:
microbiomedata/issues
public repo for issues related to NMDC work
microbiomedata/nmdc-field-notes
Mobile app for metadata collection on the go
microbiomedata/refscan
Command-line program that scans NMDC database for referential integrity violations
microbiomedata/SRA_submit
ncbi export
microbiomedata/submission-schema
microbiomedata/ReadbasedAnalysis
microbiomedata/sheets_and_friends
Enhance a LinkML model with imported and optionally modified slots
microbiomedata/metadata-for-user-facility-template-transformations
CLI tool to convert metadata submissions from the NMDC submission portal to user facility Excel templates
microbiomedata/metaT_Assembly
workflow for metatranscriptome assembly
microbiomedata/metaT_ReadCounts
microbiomedata/metaT_ReadsQC
Workflow for metatranscriptome quality control
microbiomedata/nmdc-aggregator
Scripts that periodically aggregate data related to KEGG search
microbiomedata/nmdc-datasets
Datasets that are stored in the central NMDC database.