├── .gitignore ├── README.md ├── cassiopeia-kp ├── .gitignore ├── .readthedocs.yml ├── AUTHORS.rst ├── CONTRIBUTING.rst ├── LICENSE ├── MANIFEST.in ├── README.md ├── cassiopeia │ ├── Analysis │ │ ├── __init__.py │ │ ├── reconstruct_states.py │ │ └── small_parsimony.py │ ├── ProcessingPipeline │ │ ├── __init__.py │ │ └── process │ │ │ ├── IVLT-2B_00 │ │ │ ├── IVLT-2B_00.trim.fastq │ │ │ ├── IVLT-2B_00.trim.out │ │ │ └── IVLT-2B_00.untrim.fastq │ │ │ ├── __init__.py │ │ │ ├── bam10X2fastq.pl │ │ │ ├── callAlleles-PCT-Dian.pl │ │ │ ├── callAlleles-PCT17.pl │ │ │ ├── callAlleles-PCT48.pl │ │ │ ├── changeCellBCID.py │ │ │ ├── collapse.py │ │ │ ├── collapseBam2dataFrame.pl │ │ │ ├── collapseDF2fastq.pl │ │ │ ├── collapseFastq_UMI.py │ │ │ ├── collapseUMIReadsByMSALargeFile.py │ │ │ ├── collapse_cython.c │ │ │ ├── collapse_cython.html │ │ │ ├── collapse_cython.pyx │ │ │ ├── consensusTable2fasta.pl │ │ │ ├── extractBarcodes.pl │ │ │ ├── filterMoleculeTables.py │ │ │ ├── lineageGroup.py │ │ │ ├── lineageGroup_utils.c │ │ │ ├── lineageGroup_utils.pyx │ │ │ ├── pickSeq.py │ │ │ ├── pipeline_utils.py │ │ │ ├── processBam2MT.pl │ │ │ └── processSam2MoleculeTable-PCT48_JAH.pl │ ├── TreeSolver │ │ ├── .ipynb_checkpoints │ │ │ └── compute_trees-checkpoint.sh │ │ ├── Cassiopeia_Tree.py │ │ ├── Node.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── alternative_algorithms.py │ │ ├── binarize_multistate_charmat.py │ │ ├── build │ │ │ ├── temp.linux-x86_64-2.7 │ │ │ │ ├── lineage_solver │ │ │ │ │ └── solver_utils.o │ │ │ │ └── simulation_tools │ │ │ │ │ └── dataset_generation.o │ │ │ └── temp.linux-x86_64-3.5 │ │ │ │ └── lineage_solver │ │ │ │ └── solver_utils.o │ │ ├── compute_meta_purity.py │ │ ├── compute_trees.sh │ │ ├── lineage_solver │ │ │ ├── ILP_solver.py │ │ │ ├── __init__.py │ │ │ ├── greedy_solver.py │ │ │ ├── lineage_solver.py │ │ │ ├── solution_evaluation_metrics.py │ │ │ ├── solver_utils.c │ │ │ └── solver_utils.pyx │ │ ├── post_process_tree.py │ │ ├── reconstruct_sim_tree.py │ │ ├── reconstruct_tree.py │ │ ├── sample_workflow_ivlt_simulation.py │ │ ├── sample_workflow_real_data.py │ │ ├── sample_workflow_simulated_data.py │ │ ├── score_triplets.py │ │ ├── simulate_tree.py │ │ ├── simulation_tools │ │ │ ├── __init__.py │ │ │ ├── dataset_generation.c │ │ │ ├── dataset_generation.pyx │ │ │ ├── simulation_utils.py │ │ │ └── validation.py │ │ └── utilities.pyx │ ├── __init__.py │ └── __main__.py ├── data │ ├── test_at.txt │ └── test_cm.txt ├── docs │ ├── Makefile │ ├── authors.rst │ ├── conf.py │ ├── contributing.rst │ ├── history.rst │ ├── index.rst │ ├── make.bat │ ├── readme.rst │ └── requirements.txt ├── notebooks │ ├── process_fastq.ipynb │ ├── reconstruct_lineages.ipynb │ ├── simulate_and_stress_test.ipynb │ └── theoretical_analysis.ipynb ├── scripts │ ├── .ipynb_checkpoints │ │ └── alleletable_2_charmat-checkpoint.py │ ├── .temp.txt │ ├── alleletable_2_charmat.py │ ├── alleletable_2_heatmap.py │ ├── binarize_multistate_charmat.py │ ├── calc_parsimony.R │ ├── compute_meta_chisq.py │ ├── compute_meta_purity.py │ ├── compute_tree_entropy.py │ ├── create_bootstrap.py │ ├── gestalt_reconstruct.py │ ├── lineageProfile_2_charmat.py │ ├── network_to_charmat.py │ ├── post_process_tree.py │ ├── reconstruct_tree.py │ ├── score_cci.py │ ├── score_parsimony_netx.py │ ├── score_triplets.py │ ├── shuffle_character_matrix.py │ ├── simulate_tree.py │ ├── visualize_treeheatmap_general.R │ ├── visualize_treeheatmap_nested.R │ └── visualize_treeheatmap_weissman.R ├── setup.py └── test │ ├── data.fastq │ ├── data │ ├── sim_data_allerrors.csv │ ├── sim_data_erralleles.csv │ ├── sim_data_erribc.csv │ ├── sim_data_errumi.csv │ ├── sim_data_true.csv │ └── sim_net.pkl │ ├── gurobi.log │ ├── test_error_corrections.py │ ├── test_reconstruction.py │ └── testlog ├── reproducibility ├── Figure1_S1 │ └── Figure1_S1.ipynb ├── Figure2_S2 │ ├── 3726_NT_T1_cnv_regions.ipynb │ ├── 3730_NT_T2_cnv_count.ipynb │ ├── Figure2_S2_expansions.ipynb │ ├── clonal_expansions.py │ ├── cnv_cluster.ipynb │ ├── count_cnvs.ipynb │ ├── data │ │ ├── 17_HMM_predHMMi6.rand_trees.hmm_mode-subclusters.cell_groupings │ │ ├── HMM_CNV_predictions.HMMi6.rand_trees.hmm_mode-subclusters.Pnorm_0.2.pred_cnv_regions.dat │ │ ├── cnvs_per_cell.csv │ │ ├── expansion_cnv_regions.pkl.gz │ │ ├── mm10_gene_ordering.tsv │ │ ├── nearest_neighbor_probabilities.csv │ │ └── tumors.txt │ ├── expansion_cnv_regions.ipynb │ ├── expansion_cnvs.ipynb │ ├── nearest_neighbor_probabilities.ipynb │ ├── plots │ │ ├── 3513_NT_T3_cnv_regions.pdf │ │ ├── 3730_NT_T2_cnv_count.pdf │ │ └── 3730_NT_T2_colorstrip.pdf │ └── scripts │ │ ├── cnv_regions.py │ │ ├── count_cnvs.py │ │ ├── find_all_expansions.py │ │ ├── nearest_neighbor_probabilities.py │ │ ├── run_infercnv.R │ │ └── score_fitness.py ├── Figure3_S3 │ ├── Figure3_S3_diffexp.ipynb │ ├── Figure3_S3_expression.ipynb │ ├── Figure3_S3_hotspot.ipynb │ ├── data │ │ ├── fitness_module1.txt │ │ ├── fitness_module2.txt │ │ ├── fitness_module3.txt │ │ ├── majority_vote.down_genes.sgNT.txt │ │ ├── majority_vote.up_genes.sgNT.txt │ │ ├── marjanovic_meta.tsv │ │ ├── marjanovic_signatures.tsv │ │ └── signature_scores_sgNT.tsv │ ├── integrate_normal_cells.ipynb │ └── scripts │ │ ├── compute_log2fc.jl │ │ ├── run_de_chuang_etal.R │ │ ├── run_tumor_regressions.jl │ │ ├── run_vision_NT.R │ │ ├── run_vision_marjanovic.R │ │ └── run_wilcox_de.py ├── Figure4_S4 │ ├── Figure4_S4.ipynb │ ├── data │ │ └── plasticity_scores.tsv │ └── scripts │ │ ├── compute_plasticity_indices.py │ │ ├── plasticity_scores_v2.tsv │ │ └── utilities.py ├── Figure5_S5 │ ├── Figure5_S5.ipynb │ ├── data.tar.gz │ └── scripts │ │ ├── __pycache__ │ │ └── tree_utilities.cpython-37.pyc │ │ ├── compute_dissimilarity_matrices.py │ │ ├── compute_evolutionary_couplings.py │ │ ├── run_tradeseq.r │ │ └── tree_utilities.py ├── Figure6_S6 │ ├── Figure6_S6.ipynb │ └── data │ │ ├── all_de_results.cluster9.tsv │ │ ├── evolutionary_couplings.txt │ │ └── 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