cite-encode
CommandGenerate ENCODE citations for publications, grants, and presentations
@ammawlaInstall CommandData
Command
/browse-files
List, search, and inspect ENCODE files by format, type, and assembly
> /plugin marketplace add ammawla/encode-toolkit> /plugin install encode-toolkit@ammawla
Command definition
browse-files.mdname: 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.
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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Other commands on encode-toolkit.
@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 Commanddownload-encode
CommandDownload ENCODE files (BED, FASTQ, BAM, bigWig) with MD5 verification
@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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