Command
browse-files
List, search, and inspect ENCODE files by format, type, and assembly
@ammawlaView CommandData
Command
/quality-check
Assess ENCODE experiment quality using QC metrics and audit flags
Install
> /plugin marketplace add ammawla/encode-toolkit > /plugin install encode-toolkit@ammawla
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.
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.
Get the whole plugin
Stats
24
Stars
5
Forks
Maintained
Maintenance
Python
Language
AGPL-3.0
License
1mo ago
Last commit
6mo ago
Created
Repo: ammawla/encode-toolkit
Other commands on encode-toolkit.
@ammawlaView CommandCommand
cite-encode
Generate ENCODE citations for publications, grants, and presentations
@ammawlaView CommandCommand
compare-experiments
Check if two ENCODE experiments are compatible for combined analysis
@ammawlaView CommandCommand
cross-reference
Cross-reference ENCODE data with PubMed, GEO, ClinicalTrials, and bioRxiv
@ammawlaView CommandCommand
download-encode
Download ENCODE files (BED, FASTQ, BAM, bigWig) with MD5 verification
@ammawlaView CommandCommand