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Chat with your agent about projects, recommendations, and canonical papers in Paperzilla. Use when users ask for recent project recommendations, canonical paper details, markdown-based summaries, recommendation feedback, feed export, or Atom feed URLs.
Build with and use Pi, the minimal terminal coding harness. Use for installing Pi, configuring providers/models/settings, creating Pi skills/extensions/packages/themes/prompt templates, embedding Pi through the SDK, integrating over RPC or JSON event streams, parsing sessions, or developing custom Pi providers and TUI components.
Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
DiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus SMILES/SDF/MOL2, batch docking, virtual screening, and pose-confidence interpretation. Not for binding affinity prediction.
Use when working directly with the `esm` Python SDK, ESM3 or ESMC model IDs, Forge/Biohub inference clients, or ESMFold2 folding workflows.
Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral sequence downloads, AlphaFold structures, enrichment analysis, OpenTargets, COSMIC, CELLxGENE, and 8cube mouse specificity/expression data. Best for interactive exploration and simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.
| name | paperzilla |
| description | Chat with your agent about projects, recommendations, and canonical papers in Paperzilla. Use when users ask for recent project recommendations, canonical paper details, markdown-based summaries, recommendation feedback, feed export, or Atom feed URLs. |
| license | MIT |
| metadata | {"version":"1.0","skill-author":"Paperzilla Inc"} |
Use this skill when you want to chat with your agent about projects, recommendations, and canonical papers in Paperzilla.
This is the core Paperzilla skill. It gives your agent direct access to Paperzilla data, but it does not impose a workflow or external delivery integration.
Most current profiles in this repo use the pz CLI.
If the current profile ships extra agent-specific instructions, follow those as well.
brew install paperzilla-ai/tap/pz
scoop bucket add paperzilla-ai https://github.com/paperzilla-ai/scoop-bucket
scoop install pz
Use the official Linux install guide:
See the CLI repository for source builds:
Check whether your CLI is up to date and get install-specific upgrade steps:
pz update
If detection is ambiguous, override it explicitly:
pz update --install-method homebrew
pz update --install-method scoop
pz update --install-method release
pz update --install-method source
Supported values are auto, homebrew, scoop, release, and source.
pz login
If the current profile uses pz, these are the core commands.
pz project list
pz project <project-id>
pz feed <project-id>
Useful flags:
--must-read--since YYYY-MM-DD--limit N--json--atomExamples:
pz feed <project-id> --must-read --since 2026-03-01 --limit 5
pz feed <project-id> --json
pz feed <project-id> --atom
Feed output can include existing recommendation feedback markers:
[↑] upvote[↓] downvote[★] starpz paper <paper-id>
pz paper <paper-id> --json
pz paper <paper-id> --markdown
pz paper <paper-id> --project <project-id>
pz rec <project-paper-id>
pz rec <project-paper-id> --json
pz rec <project-paper-id> --markdown
pz feedback <project-paper-id> upvote
pz feedback <project-paper-id> star
pz feedback <project-paper-id> downvote --reason not_relevant
pz feedback clear <project-paper-id>
--json for machine parsing.pz paper --markdown only returns markdown when it is already prepared.pz rec --markdown can queue markdown generation and prints a friendly retry message while it is still being prepared.--atom returns a personal feed URL for feed readers.export PZ_API_URL="https://paperzilla.ai"