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From encode-toolkit
Lists, searches, and inspects ENCODE files by format (bed, bigWig, fastq, bam), output type, assembly (GRCh38, mm10), and filters like preferred_default across experiments.
npx claudepluginhub ammawla/encode-toolkit --plugin encode-toolkitHow this command is triggered — by the user, by Claude, or both
Slash command
/encode-toolkit:browse-filesThe summary Claude sees in its command listing — used to decide when to auto-load this command
Browse and inspect ENCODE files across experiments. Use `encode_list_files` to see files within a specific experiment. Use `encode_search_files` to find file types across all experiments. Use `encode_get_file_info` for detailed metadata on a single file. Common filters: file_format (bed, bigWig, fastq, bam), output_type (IDR thresholded peaks, signal of unique reads), assembly (GRCh38, mm10), preferred_default=True for ENCODE-recommended files. Refer to the search-encode skill for detailed guidance.
/browse-filesLists, searches, and inspects ENCODE files by format (bed, bigWig, fastq, bam), output type, assembly (GRCh38, mm10), and filters like preferred_default across experiments.
/f5-classifyClassifies input files like Excel and documents by type using content-first analysis, detects gaps, generates coverage declaration with quality and risk flags. Supports --dry-run, --lang, review/approve.
/researchConducts a multi-database scientific research investigation using ToolUniverse, calling tools to look up specific claims, cross-validate, and report honest INDETERMINATE results when evidence is insufficient.
/analyseAnalyzes genetic data files (23andMe, AncestryDNA, VCF, h5ad) using ClawBio Python skills, generating local reports, figures, explanations, and follow-up suggestions.
/agent-brain-typesLists available file type presets for agent-brain indexing, showing glob patterns for Python, JavaScript, TypeScript, Go, Rust, Java, C#, C/C++, web, docs, code, etc. Supports JSON output and usage examples.
Share bugs, ideas, or general feedback.
Browse and inspect ENCODE files across experiments.
Use encode_list_files to see files within a specific experiment. Use encode_search_files to find file types across all experiments. Use encode_get_file_info for detailed metadata on a single file.
Common filters: file_format (bed, bigWig, fastq, bam), output_type (IDR thresholded peaks, signal of unique reads), assembly (GRCh38, mm10), preferred_default=True for ENCODE-recommended files.
Refer to the search-encode skill for detailed guidance.