Human Cell Atlas
An open international collaboration to create comprehensive reference maps of all human cells
Pinned Repositories
data-bundle-examples
A repository housing metadata and data files (or links to data files) that are being prepared as sample data bundles for various uses.
data-consumer-vignettes
Simple walk-throughs of interacting with the DCP as a downstream data consumer.
data-store
Design specs and prototypes for the HCA Data Storage System (DSS, "blue box")
dcp2
Shared artifacts concerning the Human Cell Atlas (HCA) Data Coordination Platform (DCP)
matrix-service
DCP Expression Matrix Service
metadata-schema
This repo is for the metadata schemas associated with the HCA
sctools
Utilities for large scale distributed single cell data processing
skylab
Soon to be deprecated in favor of broadinstitute/warp github repo. Previously: Secondary analysis pipelines
table-testing
requirements, examples, and tests for expression matrix file formats
wiki
Index of the HCA wikis and other doc resources
Human Cell Atlas's Repositories
HumanCellAtlas/metadata-schema
This repo is for the metadata schemas associated with the HCA
HumanCellAtlas/skylab
Soon to be deprecated in favor of broadinstitute/warp github repo. Previously: Secondary analysis pipelines
HumanCellAtlas/data-store
Design specs and prototypes for the HCA Data Storage System (DSS, "blue box")
HumanCellAtlas/sctools
Utilities for large scale distributed single cell data processing
HumanCellAtlas/data-consumer-vignettes
Simple walk-throughs of interacting with the DCP as a downstream data consumer.
HumanCellAtlas/matrix-service
DCP Expression Matrix Service
HumanCellAtlas/fusillade
Federated User Identity Login & Access Decision Engine
HumanCellAtlas/cloud-blobstore
Simple API that abstracts out differences between the blobstores across different cloud providers.
HumanCellAtlas/dcp-cli
DEPRECATED - HCA Data Coordination Platform Command Line Interface
HumanCellAtlas/lira
Notification listener for secondary analyses
HumanCellAtlas/pipeline-tools
Pipeline-tools for HCA DCP Secondary Analyses Service
HumanCellAtlas/upload-service
DCP Ingestion File Upload Service
HumanCellAtlas/dcp
Data Coordination Platform manifest and integration tests.
HumanCellAtlas/falcon
The workflow starter of secondary analysis service
HumanCellAtlas/ingest-validator-js
Javascript validator for HCA metadata
HumanCellAtlas/secondary-analysis
Secondary Analysis Service of the Human Cell Atlas Data Coordination Platform
HumanCellAtlas/data-monitoring-dashboard
HumanCellAtlas/data-store-scale-test
Scalability tests for the HCA Data Storage System ("blue box")
HumanCellAtlas/dcp-diag
Development and operations diagnostic tools and libraries
HumanCellAtlas/logs
Infrastructure for centralizing and indexing logs
HumanCellAtlas/schema-template-generator
Interactive UI for generating metadata schema templates
HumanCellAtlas/dcp-pyjsongen
Tools for generating random JSON data from JSON schemas.
HumanCellAtlas/matrix_semantic_map
Specification for a JSON schema to map expression matrix annotations to ontology terms
HumanCellAtlas/metadata-schema-publisher
Script for creating a repo of schemas in response to Github commits
HumanCellAtlas/connexion
Swagger/OpenAPI First framework for Python on top of Flask with automatic endpoint validation & OAuth2 support
HumanCellAtlas/eb-locustio-sample
AWS Elastic Beanstalk sample code to run the load testing tool, locust.
HumanCellAtlas/ingest-hca-to-ena
Converts and submits HCA metadata to ENA
HumanCellAtlas/ingest-staging-manager
Client for handling the creation of staging areas triggered by the ingest service
HumanCellAtlas/metadata-migration
Proof of concept library for migrating metadata.
HumanCellAtlas/metadata-spreadsheet-tools
Tools for generating metadata spreadsheets