cyberneticlibrary
← library

Query ENCODE genomics and bioinformatics

encode-toolkitpluginsetup L3★3,035
davepoon/buildwithclaude ↗
What it does

Query ENCODE genomics experiments with 20 MCP tools and 48 skills

Best for

Genomics researchers who need to search ENCODE experiments, download files reliably, and cross-correlate with disease/population databases in a single workflow.

Inputs
  • · experiment type (chip-seq, atac-seq, rna-seq, etc)
  • · organism (human, mouse, etc)
  • · cell type or tissue filter
  • · assay parameters
Outputs
  • · experiment metadata and links
  • · downloaded files with MD5 verification
  • · cross-referenced data (PubMed, GTEx, ClinVar, GWAS, gnomAD)
  • · pipeline execution results
Requires
  • · ENCODE REST API
  • · PubMed API
  • · GTEx API
  • · ClinVar API
  • · GWAS Catalog API
  • · gnomAD API
Preconditions
  • · ENCODE account or public access
  • · reference genome configured
  • · bioinformatics tools installed (samtools, bwa, etc for pipelines)
Failure modes
  • · API rate limits exceeded — queries throttled
  • · file MD5 mismatch — download corrupted or partial
  • · pipeline dependencies missing — execution fails midway
  • · cross-reference APIs unstable — some lookups timeout
Trust signals
  • · MD5 verification on downloads (data integrity)
  • · 14 database cross-references integrated
  • · 48 skills (deep domain coverage)
  • · official ENCODE REST API