/browse-files

List, search, and inspect ENCODE files by format, type, and assembly

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ammawla@ammawla

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encode-toolkit

2410 skills7 agents10 commands1 MCP

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> /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.
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What this command does when you run it.

List, search, and inspect ENCODE files by format, type, and assembly

Command definition

browse-files.md

name: browse-files
description: List, search, and inspect ENCODE files by format, type, and assembly

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.

Read it on GitHub ↗

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.

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AGPL-3.0