celltypist

library1.7.1pypypiunverified

A Python tool for semi-automatic cell type classification from single-cell RNA-seq data. It uses logistic regression models trained on diverse cell atlases. Current version is 1.7.1, with regular updates on GitHub.

ai-ml data

pip install celltypist

github ↗package ↗

INSTALL

IMPORT

SIG · CELLTYPIST

celltypist

ai-mlpythonv1.7.1

Install

29.4s avg

Import

—

Disk

847MB

Pass rate

5/ 10

Env Coverage5 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v1.7.1 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.95 runs

build_error

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 29.4s · import 0.000s · 794MB

847MB installed

● package 847MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

CellTypist

✓ from celltypist import CellTypist

✗ import celltypist

Proper class instantiation requires importing the class.

Load a pre-trained model and predict cell types from an AnnData file. Replace the file path with your own data.

from celltypist import CellTypist from celltypist import models # Download model if not present (first time) model = models.Model.load(model='Immune_All_Low.pkl') # Predict cell types transcriptome_data = 'path/to/your/data.h5ad' # replace with your file predictions = CellTypist().predict(transcriptome_data, model=model) print(predictions.cell_type.value_counts())

celltypist --version

Debug

Known issues

gotchaCellTypist models are downloaded to a cache directory (~/.celltypist/) on first use. Ensure you have write permissions.

fix

Set environment variable CELLTYPIST_CACHE_DIR to a writable path.

affects: all

breakingIn version 1.6.0, the internal model loading API changed. Old code using `models.Model.load` with version string may break.

fix

Update to newer version and use `models.Model.load(model='model_name')` without explicit version. Check model naming.

affects: <1.6.0

deprecatedUsing `CellTypist().predict()` without specifying model name may fall back to a default. This behavior is deprecated.

fix

Always supply a `model` argument explicitly.

affects: >=1.5.0

Upgrade

Version history

1.7.1latest on PyPI · released Jun 25, 2025

Audit

Dependencies

scipyrequiredUsed for model computations

numpyrequiredArray operations

pandasrequiredData handling

scikit-learnrequiredLogistic regression and utilities

matplotliboptionalHeatmap and plotting

Agent activity

15 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/Teichlab/celltypist ↗

packagehttps://pypi.org/project/celltypist/ ↗