Subsemble Cell Type Classifier

Description

Code and Extended Data for the manuscript "Cell-type classification of the tumor single-cell gene expression data using the Subsemble supervised ensemble machine learning classifier".

File Structure

├── Datasets.zip                                             // Two scRNA-seq datasets and cell type labels used for cross-validation of cell type classification performance.
│   └── li_crc_counts.tsv
│   └── li_crc_labels.txt
│   └── vangalen_aml_counts.csv
│   └── vangalen_aml_labels.csv
├── Figure_Data.zip                                          // Classification performance metrics used to generate Figures 2, 3, and 4.
│   └── Figure 2
│   └── Figure 3
│   └── Figure 4AB
│   └── Figure 4C
├── Subsemble.ipynb                                          // Jupyter notebook with example Subsemble classifier for user input.
├── skf_metrics_cc.py                                        // Python script for classification performance benchmarking using N-fold CV or LOOCV.

Citation

Chen, D., Shooshtari, P. (2022). Cell-type classification of single-cell transcriptomics using the Subsemble supervised ensemble machine learning classifier. In preparation.

License

This work is licensed under a Creative Commons Attribution 4.0 International License.