celltype-cli 0.2.1

CellType CLI — An autonomous agent for drug discovery research

celltype-cli

v0.2.0 is out — Offload GPU-accelerated tools to CellType Cloud with no additional setup. ESMFold, Boltz-2, RFdiffusion, ProteinMPNN, and more. Update now:

curl -fsSL https://raw.githubusercontent.com/celltype/celltype-agent/main/install.sh | bash

An autonomous agent for drug discovery research. Like Claude Code, but for biology.

Ask questions in natural language. celltype-cli plans the analysis, selects the right tools, executes them, validates results, and returns data-backed conclusions.

Benchmark

CellType CLI achieves 90% accuracy on BixBench-Verified-50, outperforming all existing agentic systems for computational biology.

System	Accuracy
celltype-cli (Opus 4.6)	90.0%
Phylo BiomniLab	88.7%
Edison Analysis	78.0%
Claude Code (Opus 4.6)	65.3%
OpenAI Agents SDK (GPT 5.2)	61.3%

Why ct?

• 190+ drug discovery tools — Target prioritization, compound profiling, dose-response modeling, pathway enrichment, safety assessment, clinical development, and more.
• Claude-powered reasoning — Built on the Claude Agent SDK. Claude plans multi-step research workflows, calls tools, self-corrects, and synthesizes findings.
• Managed data pipelines — One-command download of DepMap, PRISM, L1000, and proteomics datasets with auto-discovery loaders.
• 30+ database APIs — PubMed, ChEMBL, UniProt, Open Targets, ClinicalTrials.gov, Reactome, PDBe, and more — no setup required.
• Research UX — Interactive terminal with @mentions, session resume, trace logging, HTML reports, and notebook export.
• Persistent sandbox — Stateful Python and R execution across turns (pandas, scipy, gseapy, pydeseq2, BioPython).
• Open source — MIT licensed.

Installation

Quick install

curl -fsSL https://raw.githubusercontent.com/celltype/celltype-agent/main/install.sh | bash

Detects Python 3.10+, installs the latest celltype-cli release from PyPI via uv, pipx, or pip, and launches the interactive setup wizard.

Manual install

# With pipx (isolated environment, recommended)
pipx install celltype-cli

# Or with pip
pip install celltype-cli

# Or with optional scientific stacks (RDKit, scanpy, torch, etc.)
pip install "celltype-cli[all]"

# Run the setup wizard
ct setup

Authentication

# Interactive setup (recommended)
ct setup

# Or set directly
export ANTHROPIC_API_KEY="sk-ant-..."

# Non-interactive (CI/scripting)
ct setup --api-key sk-ant-api03-...

Getting Started

Basic usage

# Start interactive session
ct

# Single query
ct "What are the top degradation targets for this compound?"

# Validate setup
ct doctor

Interactive commands

Inside ct interactive mode:

• /help — command reference + examples
• /tools — list all tools with status
• /agents N <query> — run N parallel research agents
• /case-study <id> — curated multi-agent case studies
• /sessions, /resume — session lifecycle
• /copy, /export — save/share outputs
• /usage — token and cost tracking

Quick examples

Target prioritization

$ ct "I have a CRBN molecular glue. Proteomics shows it degrades
      IKZF1, GSPT1, and CK1α. Which target should I prioritize?"

Combination strategy

$ ct "My lead compound is immune-cold. What combination strategy should I use?"

Resistance biomarkers

$ ct "Build a resistance biomarker panel for my lead compound"

Key Features

190+ Domain Tools

Category	Examples
Target	Neosubstrate scoring, degron prediction, co-essentiality networks
Chemistry	SAR analysis, fingerprint similarity, scaffold clustering
Expression	L1000 signatures, pathway enrichment, TF activity, immune scoring
Viability	Dose-response modeling, PRISM screening, therapeutic windows
Biomarker	Mutation sensitivity, resistance profiling, dependency validation
Clinical	Indication mapping, population sizing, TCGA stratification
Safety	Anti-target flagging, multi-modal profiling, SALL4 risk
Literature	PubMed, OpenAlex, ChEMBL search
DNA	ORF finding, codon optimization, primer design, Golden Gate/Gibson assembly
Data APIs	MyGene, UniProt, Reactome, PDBe, ClinicalTrials.gov, and 25+ more

Data Management

# Download core datasets
ct data pull depmap        # DepMap CRISPR, mutations, expression
ct data pull prism         # PRISM cell viability
ct data pull msigdb        # Gene sets
ct data pull alphafold     # Protein structures (on-demand)

# Or point to existing data
ct config set data.depmap /path/to/depmap/
ct config set data.prism /path/to/prism/

Without local data, ct still works using 30+ database APIs.

Reports

Every query auto-saves a markdown report. Convert to branded, self-contained HTML:

ct report list              # list reports
ct report publish           # convert latest .md to .html
ct report show              # open in browser

Dark theme, responsive layout, inline CSS. No CDN, no JavaScript. Shareable via email/Slack.

Known Limitations

• Local data for some tools — Target, viability, expression, combination, biomarker tools need local DepMap/PRISM/L1000 datasets. The planner auto-excludes unavailable tools and uses API alternatives.
• Optional dependencies — RDKit (chemistry), scanpy (single-cell), torch (protein embeddings). Tools report install instructions if missing.
• API rate limits — PubMed, UniProt, Open Targets may rate-limit heavy usage.

Troubleshooting

Symptom	Fix
ct fails at startup	ct doctor
No API key	ct setup or export ANTHROPIC_API_KEY=...
Data not found	ct data pull <dataset>
Missing dependency	pip install "celltype-cli[all]"
Session lost	ct --continue (sessions auto-save)

Contributing

git clone https://github.com/celltype/cli.git
cd cli
pip install -e ".[dev]"
ct setup
pytest tests/

We welcome contributions — bug reports, feature requests, documentation improvements, and pull requests.

Enterprise & On-Premise

celltype-cli is free and open source, powered by Claude out of the box.

For pharma and biotech teams that need to keep data on-premise, CellType offers proprietary research agent models purpose-built to replace frontier LLMs — deployable locally behind your firewall with zero data leaving your infrastructure.

Contact us to learn more.

License

MIT — see LICENSE

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Built by CellType Inc.