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HCA Wrangler Docs
SOPs
Introduction
Wrangling Project Management
Wrangling datasets SOP
Secondary review
HCA metadata structure
Wrangling Task tracker
Access terra
Submission variations based on request types
Wrangling Process Diagram
Metadata spreadsheet
Wrangler Spreadsheet guide
Wrangling best practices
Contributor spreadsheet quick guide
Spreadsheet examples
Access data files
Download data from Globus
AWS User for Contributors
NCBI cloud delivery SOP
Download Data from Node SOP
Download Data from Dryad 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
Update a project
Data retraction
HCA to SCEA Guide
Resolve TDR issues
Update corrupted files in TDR
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
Ingest programmatic submission
Tier 2
Tools
Download from archives
Downloading 10x BAM files from archives
Downloading and converting SRA objects from SRA
Downloade GEO supplementary files
Uploading files to an s3 bucket from the archives
Download files using aspera
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 yaml to csv
Extract all text to ontology mappings
Validate files in ec2
cypher query snippets
All snippets
EBI wrangler onboarding
HCA wrangler docs visual index
Technology type metadata
Tier 2 - Resources
Tier 2 definitions
Edit these Docs on GitHub
SOPs
Tier 2
Tier 2
Here you can find SOPs on how to navigate across tier 2 definitions and resources