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HCA Wrangler Docs
SOPs
Introduction
Wrangling datasets SOP
Secondary review
HCA metadata structure
Access terra
Triage
Dataset acknowledgement SOP
Dataset Suitability
Dataset Triage SOP
GDPR_Guidelines
Metadata spreadsheet
Wrangler Spreadsheet guide
Wrangling best practices
GEO to HCA Guide
Contributor spreadsheet quick guide
Spreadsheet examples
Access data files
Download data from Globus
NCBI cloud delivery SOP
Download Data from Node SOP
Managed access
Data Contributor Agreement explained
Data Contributor Agreement SOP
Pre-submission SOP
Data Transfer SOP
Data and metadata review and export SOP
Contributor communication
After export
Archiving
Data retraction
Update a project
Update ENA runs
HCA to SCEA Guide
Update schema & ontology
Request ontology terms
Schema update prioritisation
Update Zooma Data source
Technology Types Guide
10X - Visium
How to curate 10X Visium Gene Expression Data
10X Spatial Transcriptomics
CITE-Seq
How to curate CITE-seq Gene Expression & Surface Protein Data
CITE-seq - Cellular Indexing of Transcriptomes and Epitopes by Sequencing
NanoString Spatial Profiling
Overview of NanoString Digital Spatial Profiling and RNAScope
scATAC-seq
How to curate scATAC-seq Data
scATAC-seq - Single-cell sequencing assay for transposase-accessible chromatin
Advanced & other SOPs
Contributor matrix and cell types
Ingest programmatic submission
Cloud cost report
Tools
Download from archives
Downloading 10x files from archives
Downloading and converting SRA objects from SRA
Uploading files to an s3 bucket from the archives
Accessing upload area
hca-util tool
Transfer files between local and EC2 - cyberduck
Transfer files between local and EC2 - scp, rsync
Useful commands
Converting markdown to pdf - grip
Terminal sessions in EC2 - tmux, screen
git commands
Useful scripts
Converting JSON schema properties to csv
Converting yaml to csv
Extract all text to ontology mappings
Generate submission summary report
Validate files in ec2
cypher query snippets
hca_cli_commands
All snippets
EBI wrangler onboarding
HCA wrangler docs visual index
Technology type metadata
Edit these Docs on GitHub
SOPs
Technology Types Guide
Technology Types Guide
Here are some guidelines for wrangling specific technologies.
Table of contents
10X - Visium
CITE-Seq
NanoString Spatial Profiling
scATAC-seq