Original code developed for Geßner, Jolly et al
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ABCLeukemogenesisModelselection.ipynb is a jupyter notebook containing the whole dynamical modeling procedure (ODE model, clones*parameters matrix construction, Approximate Bayesian Computation parameter inference with pyABC).
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BarcodeExtraction.r: pipeline for the extraction and filtering of lineage barcode sequences generated as described in the manuscript, and then add the barcode information to a Bioconductor SingleCellExperiment object. The Barcodes are extracted from a BAM file containing exclusively lineage barcode sequences assigned to single-cells.
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XGboostTrainingandModelTesting.r : pipeline for learning the clone classification model with XGBoost as described in the manuscript and then testing the statistical significance of the model predictions by label permutations.