Welcome to CellTypist’s documentation!
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.
Install CellTypist
Using pip
pip install celltypist
Using conda
conda install -c bioconda -c conda-forge celltypist
Changelog
CellTypist 1.6.2 (November 1, 2023)
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.annotateAdd gene symbol to ID conversion file and expand README #87
CellTypist 1.6.0 (August 5, 2023)
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 #29Raise 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