browse-files
CommandList, search, and inspect ENCODE files by format, type, and assembly
@ammawlaInstall CommandData
Command
/compare-experiments
Check if two ENCODE experiments are compatible for combined analysis
> /plugin marketplace add ammawla/encode-toolkit> /plugin install encode-toolkit@ammawla
Command definition
compare-experiments.mdname: compare-experiments description: Check if two ENCODE experiments are compatible for combined analysis
Compare two ENCODE experiments to determine if they can be analyzed together.
Both experiments must be tracked first with `encode_track_experiment`. Then use `encode_compare_experiments` to check organism, assembly, assay type, biosample, organ, target, replication type, and lab compatibility. It returns a verdict with issues, warnings, and recommendations.
Refer to the compare-biosamples skill for cross-biosample comparisons.
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 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 Commandmanage-credentials
CommandStore, check, or clear ENCODE API credentials for restricted 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