Welcome to CellTypist’s documentation!

Python Versions Documentation Status

CellTypist is an automated cell type annotation tool for scRNA-seq datasets on the basis of logistic regression classifiers optimised by the stochastic gradient descent algorithm. CellTypist allows for cell prediction using either built-in (with a current focus on immune sub-populations) or custom models, in order to assist in the accurate classification of different cell types and subtypes.

CellTypist website

Information of CellTypist can be also found in our CellTypist portal. Website www.celltypist.org

Install CellTypist

Using pip PyPI

pip install celltypist

Using conda install with bioconda

conda install -c bioconda -c conda-forge celltypist


CellTypist 1.6.3 (June 6, 2024)

  • GPU support based on rapids-singlecell during the over-clustering step #110

  • Load custom model directly #60

CellTypist 1.6.2 (November 1, 2023)

  • Reformat error and warning messages during prediction #89

  • Fix cuml import during model training

  • Fix categorical output from new versions of pandas during majority voting #96

CellTypist 1.6.1 (September 25, 2023)

  • Add cuML-based GPU support for model training #80

  • Detect data input format only for the first 1000 cells

  • Fix KeyError in to_adata when setting mode = 'prob match' in celltypist.annotate

  • Add gene symbol to ID conversion file and expand README #87

CellTypist 1.6.0 (August 5, 2023)

  • Separate CellHint from CellTypist

  • Keep strict one-to-one orthologs during species model conversion

  • Auto-fetch feature transfer files for model conversion

  • Adapt code to sklearn>=1.3.0 #75

CellTypist 1.5.3 (July 10, 2023)

  • Fix DistanceMetric import for sklearn >= 1.3.0 #73

  • Detect input format for celltypist.dotplot

  • Require leidenalg >= 0.9.0

CellTypist 1.5.2 (June 8, 2023)

  • Patch log1p serialization issue and model download error

CellTypist 1.5.1 (May 26, 2023)

  • Fix error in not importing spmatrix in pct

CellTypist 1.5.0 (May 16, 2023)

A more mature release before the formal CellTypist v2

CellTypist 1.4.0 (May 2, 2023)

  • Add modules of cell type harmonisation and integration (a release before the formal CellTypist v2)

CellTypist 1.3.0 (December 14, 2022)

  • Transfer numpy matrix to array during prediction for compatibility with sklearn >= 1.0 #50

CellTypist 1.2.0 (August 22, 2022)

  • Report all model url request errors (including timeout error) #28

  • Add with_mean parameter in celltypist.train to optimize RAM usage by not subtracting the mean #29

  • Raise warning instead of error during prediction when the input expression matrix contains only a subset of genes

  • Reformat docs with independent pages for main functions

  • Support dot plot when the prediction comes from the ‘prob match’ mode #33

  • Disable hard-coded max_iter in celltypist.train with default values varying according to dataset sizes

CellTypist 1.1.0 (June 09, 2022)

  • Add citation (PMID: 35549406)

  • Add Docker/Singularity container

  • Fix the error of celltypist.dotplot when reference cluster is type of int #22

  • Relax the criteria of detecting the plain file format

  • Expand the docstring of convert to explicitly support gene name transfer #26

  • Automatically transpose (with warning) the input gene-by-cell matrix instead of raising an error

CellTypist 1.0.0 (May 12, 2022)

CellTypist 1.0.0

CellTypist 0.2.1 (Apr 24, 2022)

Final beta version

CellTypist 0.2.0 (Feb 12, 2022)

Closer-to-mature version

CellTypist 0.1.9 (Dec 14, 2021)

Close-to-mature version