browse-files
CommandList, search, and inspect ENCODE files by format, type, and assembly
@ammawlaInstall CommandData
Command
/search-encode
Search ENCODE experiments by assay, organ, biosample, or target
> /plugin marketplace add ammawla/encode-toolkit> /plugin install encode-toolkit@ammawla
Command definition
search-encode.mdname: search-encode description: Search ENCODE experiments by assay, organ, biosample, or target
Search the ENCODE Project for experiments matching the user's criteria.
Use the `encode_search_experiments` tool with filters like assay_title, organ, biosample_term_name, and target. Start with `encode_get_facets` if the user is exploring what data exists. Use `encode_get_metadata` to discover valid filter values.
Refer to the search-encode skill for detailed guidance.
Ships withencode-toolkit
Search ENCODE, cross-reference 14 databases, run 7 analysis pipelines, and generate publication-ready methods — all from natural language in Claude Code.
2047 skills7 agents1 MCP
Stars on GitHub
Momentum
- stars in total
- 20
Other commands on encode-toolkit.
@ammawlaInstall Commandcite-encode
CommandGenerate ENCODE citations for publications, grants, and presentations
@ammawlaInstall Commandcompare-experiments
CommandCheck if two ENCODE experiments are compatible for combined analysis
@ammawlaInstall Commandcross-reference
CommandCross-reference ENCODE data with PubMed, GEO, ClinicalTrials, and bioRxiv
@ammawlaInstall Commanddownload-encode
CommandDownload ENCODE files (BED, FASTQ, BAM, bigWig) with MD5 verification
@ammawlaInstall Commandlog-provenance
CommandLog derived files and trace provenance back to ENCODE source data
@ammawlaInstall CommandMore commands from other plugins.
Auto-invoked
recall
CommandSearch past session observations and lessons for relevant context. Wrap the `memory_smart_search` and `memory_lesson_recall` MCP…
@rohitg00Install Commandcreate-skill
CommandCreate an AI skill from any source (URL, repo, PDF, video, notebook, etc.)
@yusufkaraaslanInstall Command