browse-files
CommandList, search, and inspect ENCODE files by format, type, and assembly
@ammawlaInstall CommandData
Command
/download-encode
Download ENCODE files (BED, FASTQ, BAM, bigWig) with MD5 verification
> /plugin marketplace add ammawla/encode-toolkit> /plugin install encode-toolkit@ammawla
Command definition
download-encode.mdname: download-encode description: Download ENCODE files (BED, FASTQ, BAM, bigWig) with MD5 verification
Download ENCODE data files to a local directory.
Use `encode_batch_download` with `dry_run=True` first to preview files. Then set `dry_run=False` to download. For specific files, use `encode_download_files` with file accessions. Always verify MD5 checksums.
Refer to the download-encode 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.
2047 skills7 agents1 MCP
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Other commands on encode-toolkit.
@ammawlaInstall Commandcite-encode
CommandGenerate ENCODE citations for publications, grants, and presentations
@ammawlaInstall Commandcompare-experiments
CommandCheck if two ENCODE experiments are compatible for combined analysis
@ammawlaInstall Commandcross-reference
CommandCross-reference ENCODE data with PubMed, GEO, ClinicalTrials, and bioRxiv
@ammawlaInstall Commandlog-provenance
CommandLog derived files and trace provenance back to ENCODE source data
@ammawlaInstall Commandmanage-credentials
CommandStore, check, or clear ENCODE API credentials for restricted data
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