Installation
API
User guide
Contributing
Credits
References
GitHub
Twitter
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.get_lca_characters
cassiopeia.data.sample_bootstrap_allele_tables
cassiopeia.data.sample_bootstrap_character_matrices
cassiopeia.data.to_newick
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.SupercellularSampler
cassiopeia.sim.UniformLeafSubsampler
Plotting
cassiopeia.pl.upload_and_export_itol
API
ΒΆ
Import Cassiopeia as:
import
cassiopeia
as
cas
Preprocess
Data
Solver
Simulator
Plotting
Installation
Preprocess