/compare-experiments
Check if two ENCODE experiments are compatible for combined analysis
$ npx -y skills add ammawla/encode-toolkit --agent claude-codeShips with encode-toolkit. Installing the plugin gets this command.
How it fires
How this command gets triggered: by you, by Claude, or both.
- Fires itselfClaude auto-loads it when your prompt matches the work.
- You can call itInvoke it directly when you want it.
- Slash command
/compare-experiments
Context preview
What this command does when you run it.
Check if two ENCODE experiments are compatible for combined analysis
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, target, and replication compatibility.
Refer to the compare-biosamples skill for cross-biosample comparisons.
Search ENCODE, cross-reference 14 databases, run 7 analysis pipelines, and generate publication-ready methods — all from natural language in Claude Code.
Repo: ammawla/encode-toolkit
Other commands on encode-toolkit.
- /browse-files
List, search, and inspect ENCODE files by format, type, and assembly
Open command - /cite-encode
Generate ENCODE citations for publications, grants, and presentations
Open command - /cross-reference
Cross-reference ENCODE data with PubMed, GEO, ClinicalTrials, and bioRxiv
Open command - /download-encode
Download ENCODE files (BED, FASTQ, BAM, bigWig) with MD5 verification
Open command - /log-provenance
Log derived files and trace provenance back to ENCODE source data
Open command - /manage-credentials
Store, check, or clear ENCODE API credentials for restricted data
Open command