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  • Installation
  • API
  • User guide
  • Contributing
  • Credits
  • References

Site Navigation

  • Installation
  • API
  • User guide
  • Contributing
  • Credits
  • References

Section Navigation

  • Preprocess
    • cassiopeia.pp.align_sequences
    • cassiopeia.pp.call_alleles
    • cassiopeia.pp.call_lineage_groups
    • cassiopeia.pp.collapse_umis
    • cassiopeia.pp.convert_fastqs_to_unmapped_bam
    • cassiopeia.pp.error_correct_cellbcs_to_whitelist
    • cassiopeia.pp.error_correct_intbcs_to_whitelist
    • cassiopeia.pp.error_correct_umis
    • cassiopeia.pp.filter_bam
    • cassiopeia.pp.filter_molecule_table
    • cassiopeia.pp.filter_cells
    • cassiopeia.pp.filter_umis
    • cassiopeia.pp.resolve_umi_sequence
    • cassiopeia.pp.compute_empirical_indel_priors
    • cassiopeia.pp.convert_alleletable_to_character_matrix
    • cassiopeia.pp.convert_alleletable_to_lineage_profile
    • cassiopeia.pp.convert_lineage_profile_to_character_matrix
  • Data
    • cassiopeia.data.CassiopeiaTree
    • cassiopeia.data.compute_dissimilarity_map
    • cassiopeia.data.compute_phylogenetic_weight_matrix
    • cassiopeia.data.get_lca_characters
    • cassiopeia.data.sample_bootstrap_allele_tables
    • cassiopeia.data.sample_bootstrap_character_matrices
    • cassiopeia.data.to_newick
  • Critique
    • cassiopeia.critique.robinson_foulds
    • cassiopeia.critique.triplets_correct
  • Solver
    • cassiopeia.solver.HybridSolver
    • cassiopeia.solver.ILPSolver
    • cassiopeia.solver.MaxCutSolver
    • cassiopeia.solver.MaxCutGreedySolver
    • cassiopeia.solver.NeighborJoiningSolver
    • cassiopeia.solver.PercolationSolver
    • cassiopeia.solver.SharedMutationJoiningSolver
    • cassiopeia.solver.SpectralSolver
    • cassiopeia.solver.SpectralGreedySolver
    • cassiopeia.solver.UPGMASolver
    • cassiopeia.solver.VanillaGreedySolver
    • cassiopeia.solver.dissimilarity_functions.cluster_dissimilarity
    • cassiopeia.solver.dissimilarity_functions.hamming_distance
    • cassiopeia.solver.dissimilarity_functions.hamming_similarity_normalized_over_missing
    • cassiopeia.solver.dissimilarity_functions.hamming_similarity_without_missing
    • cassiopeia.solver.dissimilarity_functions.weighted_hamming_distance
    • cassiopeia.solver.dissimilarity_functions.weighted_hamming_similarity
  • Simulator
    • cassiopeia.sim.BirthDeathFitnessSimulator
    • cassiopeia.sim.CompleteBinarySimulator
    • cassiopeia.sim.SimpleFitSubcloneSimulator
    • cassiopeia.sim.Cas9LineageTracingDataSimulator
    • cassiopeia.sim.BrownianSpatialDataSimulator
    • cassiopeia.sim.ClonalSpatialDataSimulator
    • cassiopeia.sim.SupercellularSampler
    • cassiopeia.sim.SpatialLeafSubsampler
    • cassiopeia.sim.UniformLeafSubsampler
  • Plotting
    • cassiopeia.pl.labels_from_coordinates
    • cassiopeia.pl.plot_matplotlib
    • cassiopeia.pl.plot_plotly
    • cassiopeia.pl.Tree3D
    • cassiopeia.pl.upload_and_export_itol
  • Tools
    • cassiopeia.tl.compute_morans_i
    • cassiopeia.tl.IIDExponentialBayesian
    • cassiopeia.tl.IIDExponentialMLE
    • cassiopeia.tl.compute_evolutionary_coupling
    • cassiopeia.tl.calculate_likelihood_continuous
    • cassiopeia.tl.calculate_likelihood_discrete
    • cassiopeia.tl.calculate_parsimony
    • cassiopeia.tl.estimate_missing_data_rates
    • cassiopeia.tl.estimate_mutation_rate
    • cassiopeia.tl.fitch_count
    • cassiopeia.tl.fitch_hartigan
    • cassiopeia.tl.score_small_parsimony
    • cassiopeia.tl.compute_expansion_pvalues
  • API

API#

Import Cassiopeia as:

import cassiopeia as cas
  • Preprocess
  • Data
  • Critique
  • Solver
  • Simulator
  • Plotting
  • Tools

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