ingest
Lite ingest — fetch a paper and write a short 4-section triage summary (Key Takeaways, Background, Main Idea & Summary, Critique). No figures, fast.
A command is the one you type. It runs exactly when you ask it to, and never before.
25 commands across 241 plugins.
Lite ingest — fetch a paper and write a short 4-section triage summary (Key Takeaways, Background, Main Idea & Summary, Critique). No figures, fast.
Scaffold a new PaperLoom at the configured path (or at an optional path argument). Idempotent — fills missing files without clobbering existing ones.
Scan the vault for orphan pages, frontmatter schema drift, duplicate findings, unmarked contradictions, and stale wikilinks. Reports issues without auto-fixing.
Opens a link to join the Pinecone Discord, allowing users to learn from each other, contact the Pinecone team, and get help in our dedicated help channel.
List, search, and inspect ENCODE files by format, type, and assembly
Generate ENCODE citations for publications, grants, and presentations
Check if two ENCODE experiments are compatible for combined analysis
Design a BigQuery table schema with optimal partitioning, clustering, and data types. Describe your data or paste a sample.
Estimate the cost of a BigQuery query or table. Pass a query, file path, or table description.
Explain a BigQuery feature, function, or concept with working examples. Pass the feature name or question.
Ask a mind-clone of an author — advice, or their likely view on a topic
Build a mind-clone of an author from their public content
Ask a question of the research vault. Searches papers and findings, synthesizes an answer with wikilink citations.
Cross-reference ENCODE data with PubMed, GEO, ClinicalTrials, and bioRxiv
Download ENCODE files (BED, FASTQ, BAM, bigWig) with MD5 verification
Log derived files and trace provenance back to ENCODE source data
Generate optimized BigQuery SQL from a natural language description. Pass a description of the data you need.
Optimize BigQuery SQL by fixing all detected anti-patterns. Pass a file path or paste SQL directly.
Review BigQuery SQL for performance anti-patterns. Pass a file path or paste SQL directly.
Store, check, or clear ENCODE API credentials for restricted data
Assess ENCODE experiment quality using QC metrics and audit flags
Search ENCODE experiments by assay, organ, biosample, or target
Track ENCODE experiments locally with publications and provenance
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