/quality-check
Assess ENCODE experiment quality using QC metrics and audit flags
$ 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
/quality-check
Context preview
What this command does when you run it.
Assess ENCODE experiment quality using QC metrics and audit flags
Command definition
quality-check.mdname: quality-check description: Assess ENCODE experiment quality using QC metrics and audit flags
Evaluate data quality for ENCODE experiments using standard metrics: FRiP, NSC, RSC for ChIP-seq; TSS enrichment for ATAC-seq; mapping rate for RNA-seq.
Use `encode_get_experiment` to retrieve audit information. Check for ERROR and NOT_COMPLIANT audit flags. Always require 2+ biological replicates.
Refer to the quality-assessment skill for detailed guidance.
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 - /compare-experiments
Check if two ENCODE experiments are compatible for combined analysis
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