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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
HCA wrangler docs visual index
Legend
P1.
Acknowledgement
P4.
assign primary wrangler
A1.
make contact
send questionnaires
C1.
complete T&C & data questionnaires
S3.
validate spreadsheet
A4.
request final
approval
C4.
approve
A2.
Generate & send spreadsheet & upload area
S5.
submit to ingest
pre-archived
S2.
upload data to ingest
I1.
submit to DSP
ENA, BioStudies, BioSamples
I2.
Collect Accessions
A5.
communicate accessions
C5.
submit accessions with manuscript
DCP 2.0
A6.
Convert to MAGE-TAB
A7.
Facilitate submission to ArrayExpress & SCEA
C2.
fill out spreadsheet
active
A3.
curate spreadsheet
wrangler owned tools
ingest owned tools
ingest-archiver
HCA-SCEA toola
GEO-to-HCA
S1.
create upload area
B3.
transfer raw data to upload area
tools with no owner
wrangler actions
contributor actions
ingest dev actions
published data
flow
active wrangling
flow
P2.
assess suitability
tracking spreadsheet
hca-util
contributor
B1.
auto-fill spreadsheet
B2.
curate spreadsheet
S4.
request review
C3.
upload raw data to upload area
perform review
Secondary wrangler
Triage and suitability
shared
ingest
hca-util
schema-template-generator
Google forms
ingest-ui
ingest-exporter
EBI Archives
hca-util
P3.
prioritise
hca-util
Edit this diagram here