clacell 0.1.0

robust cell type classifier for immune cells

CLACELL

Robust cell type classifier for immune cells

Usage

MarkerAnnotator

The MarkerAnnotator can be used to annotate an Anndata dataset. It uses a marker based annotation strategy to annotate the dataset. You can either use an own marker dictionary or use the default dictionary.

from clacell import MarkerAnnotator

annotator = MarkerAnnotator(marker_dict=marker_dict)
adata = annotator.annotate(adata)
# Now adata.obs['scumi-annotation'] contains the annotations

BloodCellClassifier

The cell type classifier has four different methods:

1. grid_search: Makes a search over the hyperparameters of the model, evaluates the best model and retrains it on the whole dataset using 'train'.
2. train: Trains the model with the given hyperparameters.
3. evaluate: Evaluates the current model with robustness tests. The model needs to be trained before this method is called.
4. predict: Predicts new samples. The model needs to be trained before this method is called.

All methods can be called with Dataframes or with an Anndata object. If an Anndata object is provided, it will be automatically preprocessed.

from clacell import BloodCellClassifier

classifier = BloodCellClassifier()

# 1. GridSearch
print("\n1. grid_search")
classifier.grid_search(X_train, y_train, X_test, y_test, n_jobs=3)

# 2. Train
print("\n2. train")
classifier.train(X_train, y_train, C=0.001)

# 3. Evaluate
print("\n3. evaluate")
classifier.evaluate(X_test, y_test)

# 4. Predict
print("\n4. predict")
predictions = classifier.predict(X_test)
print(f"Macro F1: {f1_score(y_test, predictions, average="macro")}")

Acknowledgments & Data Sources

The marker based annotation strategy is a reimplementation of the existing R package scumi-dev (licensed under BSD 3-Clause License). Link to the repository: https://bitbucket.org/jerry00/scumi-dev/src/master/

• Citation: Ding, J., Adiconis, X., Simmons, S.K. et al. Systematic comparison of single-cell and single-nucleus RNA-sequencing methods. Nat Biotechnol 38, 737–746 (2020). https://doi.org/10.1038/s41587-020-0465-8

This repository contains reference datasets used for training and validation:

• CellTypist: The Cross-tissue Immune Cell Atlas was provided by the Teichmann Group at the Wellcome Sanger Institute and were hosted by Genome Research Limited (licensed under CC BY-NC-ND 4.0). Link: https://www.tissueimmunecellatlas.org/
  • Citation: C. Domínguez Conde et al., Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science376, eabl5197(2022).DOI: 10.1126/science.abl5197
• Human Cell Atlas (HCA): HematopoieticImmuneCellAtlas (licensed under CC-BY 4.0). Project Link: https://explore.data.humancellatlas.org/projects/cc95ff89-2e68-4a08-a234-480eca21ce79
  • Citation: Li, B., Kowalczyk, M.S. et al. Hematopoietic Immune Cell Atlas. Human Cell Atlas Data Portal (2026).