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 1.1.0 (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