Cross-reference NCBI GEO with ENCODE experiments
geo-connectorskillsetup L2★35
ammawla/encode-toolkit ↗What it does
Query and cross-reference NCBI GEO with ENCODE datasets
Best for
Finding complementary expression datasets in GEO that validate or extend ENCODE regulatory findings
Inputs
- · ENCODE experiment accession
- · GEO accession (GSE/GSM)
- · search term
Outputs
- · GEO metadata
- · complementary datasets
- · series matrices
Requires
- · NCBI E-utilities API
- · GEO acc.cgi endpoint
- · FTP GEO
- · SRA
Preconditions
NCBI email/API key for rate limiting (optional, 3 req/sec without)
Failure modes
- · API rate limiting on large batch queries
- · Missing GEO cross-references in ENCODE
- · SOFT format parsing complexity
Trust signals
- · NCBI official E-utilities documented
- · Detailed GEO entity hierarchy
- · Real query examples