CyteType

Agentic, Evidence-Based Cell Type Annotation for Single-Cell RNA-seq

CI Status Python Version PyPI version License: CC BY-NC-SA 4.0 PyPI downloads

CyteType is an end-to-end cell type annotation system for single-cell RNA sequencing (scRNA-seq), designed for repeatable analysis pipelines rather than one-off prompting. It combines cluster-level marker genes, expression context, study metadata, literature retrieval, ontology mapping, and a dedicated review step in a structured workflow that operates directly on AnnData.

For Seurat workflows, use CyteTypeR.

[!IMPORTANT] Already installed CyteType? Open a terminal and run pip install -U cytetype to update to the latest version before you start.

CyteType requires an API key. Use is free for academic and non-commercial research. Commercial use requires a license.

Quick Start

1. Install

pip install cytetype

2. Set up your API key

cytetype setup

This opens passwordless CyteType sign-in in your browser and saves the API key locally for automatic use from Python. You can also create or manage API keys in the dashboard.

Already have an API key? Save and validate it locally once:

cytetype login

3. Annotate with Scanpy

import scanpy as sc
from cytetype import CyteType

# Assumes preprocessed AnnData with clusters and marker genes
group_key = "clusters"
annotator = CyteType(
    adata,
    group_key=group_key,
    rank_key=f"rank_genes_{group_key}",
    n_top_genes=100,
)
adata = annotator.run(study_context="Human PBMC from a healthy donor")
sc.pl.umap(adata, color="cytetype_annotation_clusters")

Try CyteType in Google Colab.

What You Get

  • Annotations: Cell type, subtype, and activation state for every cluster
  • Cell Ontology mapping: Standardized CL IDs for comparison across studies
  • Confidence and quality control: Confidence values, plus match scores against your existing labels
  • Supporting evidence: Publications and condition-specific references behind each call

Example Report

Each analysis generates an HTML report with annotation decisions, reviewer comments, supporting evidence, and an embedded chat interface connected to your expression data.

CyteType HTML report showing cell type annotations marker genes

View example report

Benchmarks

Across PBMC, bone marrow, tumor microenvironment, and cross-species datasets, the multi-agent approach outperforms existing annotation methods:

Compared with Improvement
GPTCellType +388%
CellTypist +268%
SingleR +101%

Methods and full results are in the preprint. You can also browse results on atlas-scale datasets.

Resources

Citation

Ahuja G, Antill A, Su Y, Dall'Olio GM, Basnayake S, Karlsson G, Dhapola P. Multi-agent AI enables evidence-based cell annotation in single-cell transcriptomics. bioRxiv 2025. doi: 10.1101/2025.11.06.686964

@article{cytetype2025,
  title={Multi-agent AI enables evidence-based cell annotation in single-cell transcriptomics},
  author={Gautam Ahuja, Alex Antill, Yi Su, Giovanni Marco Dall'Olio, Sukhitha Basnayake, Göran Karlsson, Parashar Dhapola},
  journal={bioRxiv},
  year={2025},
  doi={10.1101/2025.11.06.686964},
  url={https://www.biorxiv.org/content/10.1101/2025.11.06.686964v1}
}

License

CyteType is free for academic and non-commercial research under CC BY-NC-SA 4.0.

For commercial licensing, contact contact@nygen.io.

Project links

Data verified by PyPI on Aug 11, 2026
Data provided by the project maintainers, verified at the time the release was uploaded to PyPI.

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for parashardhapola from gravatar.com parashardhapola

Credits

Author: Parashar Dhapola

GitHub Statistics

Data verified by PyPI on Aug 11, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

CC BY-NC-SA 4.0

Requires

Python >=3.12

Tags

bioinformatics single-cell RNA-seq annotation cell types

Report project as malware

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

cytetype-0.20.1.tar.gz (227.3 kB view details)

Uploaded Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

cytetype-0.20.1-py3-none-any.whl (88.2 kB view details)

Uploaded Python 3

File details

Details for the file cytetype-0.20.1.tar.gz.

File metadata

  • Download URL: cytetype-0.20.1.tar.gz
  • Upload date:
  • Size: 227.3 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/7.0.0 CPython/3.13.14

File hashes

Hashes for cytetype-0.20.1.tar.gz
Algorithm Hash digest
SHA256 2b6d76703c1e051c189ee0b7240b0f3f918489fa61d0ac2fef26e512f83f592d
MD5 fc26ac6aa5274aca8a3f067145b43e7b
BLAKE2b-256 979b0a0cb3241fa82d1d10e11c90a574e9dea7d4f719e5cd88ca9ef0d7a3c697

See more details on using hashes here.

Provenance

The following attestation bundles were made for cytetype-0.20.1.tar.gz:

Publisher: publish.yml on NygenAnalytics/CyteType

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

File details

Details for the file cytetype-0.20.1-py3-none-any.whl.

File metadata

  • Download URL: cytetype-0.20.1-py3-none-any.whl
  • Upload date:
  • Size: 88.2 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/7.0.0 CPython/3.13.14

File hashes

Hashes for cytetype-0.20.1-py3-none-any.whl
Algorithm Hash digest
SHA256 a7d14d23af04752b8a96f20b9bbad7c98484a38d50eb5e6bc50b207bcf631623
MD5 1036d217d674975400c99d94ec7b5685
BLAKE2b-256 9b6af8f6267971f4d5acb8c9360bfd04170e2b198afc5f4d4c054882d205a624

See more details on using hashes here.

Provenance

The following attestation bundles were made for cytetype-0.20.1-py3-none-any.whl:

Publisher: publish.yml on NygenAnalytics/CyteType

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Release history Release notifications | RSS feed

This release

0.20.1 This release

2 files

0.19.5

2 files

0.19.4

2 files

0.19.3

2 files

0.19.2

2 files

0.19.1

2 files

0.19.0

2 files

0.18.1

2 files

0.18.0

2 files

0.17.0

2 files

0.16.1

2 files

0.16.0

2 files

0.15.0

2 files

0.14.1

2 files

0.13.0

2 files

0.12.0

2 files

0.11.0

2 files

0.10.0

2 files

0.9.2

2 files

0.9.1

2 files

0.9.0

2 files

0.8.3

2 files

0.8.1

2 files

0.8.0

2 files

0.7.0

2 files

0.6.2

2 files

0.6.1

2 files

0.6.0

2 files

0.5.2

2 files

0.5.1

2 files

0.5.0

2 files

0.4.0

2 files

0.3.5

2 files

0.3.4

2 files

0.3.3

2 files

0.3.2

2 files

0.3.1

2 files

0.3.0

2 files

0.2.1

2 files

0.2.0

2 files

0.1.4

2 files

0.1.3

2 files

0.1.2

2 files

0.1.1

2 files

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Depot Continuous Integration Fastly CDN Google Download Analytics Sentry Error logging StatusPage Status page