DCLEAR                  DCLEAR: A package for DCLEAR: Distance based
                        Cell LinEAge Reconstruction
WH                      WH
WH_train                Train weights for WH
WH_train_fit            Train weights for WH, and output distance
                        object
add_deletion            add_deletion
add_dropout             add_dropout
as_igraph               Generic function for as_igraph
as_igraph,data.frame-method
                        as_igraph
as_igraph,phylo-method
                        as_igraph
as_lineage_tree         Generic function for as_lineage_tree
as_lineage_tree,phyDat,phylo,lineage_tree_config-method
                        as_lineage_tree
as_phylo                Generic function for as_phylo
as_phylo,igraph-method
                        as_phylo
dist_kmer_replacement_inference
                        Core function of computing kmer replacement
                        distance
dist_replacement        Generic function for dist_replacement
dist_replacement,phyDat,kmer_summary,integer-method
                        Compute the kmer replacement distance
dist_replacement,phyDat,missing,integer-method
                        Compute the kmer replacement distance
dist_weighted_hamming   Generic function for dist_weighted_hamming
dist_weighted_hamming,phyDat,numeric-method
                        dist_weighted_hamming
downsample              Generic function for downsample
downsample,igraph-method
                        downsample
downsample,lineage_tree-method
                        downsample
get_distance_prior      get_distance_prior
get_leaves              Generic function for get_leaves
get_leaves,lineage_tree-method
                        get_leaves
get_node_names          get_node_names
get_replacement_probability
                        get_replacement_probability
get_sequence            get_sequence
get_transition_probability
                        get_transition_probability
lineages                Lineage data
positional_mutation_prob
                        positional_mutation_prob
process_sequence        Generic function for process_sequence
process_sequence,phyDat-method
                        Process sequences
prune                   Generic function for prune
prune,igraph-method     prune
prune,lineage_tree-method
                        prune
random_tree             random_tree
rbind,phyDat-method     rbind
sample_mutation_outcome
                        sample_mutation_outcome
sample_mutation_site    sample_mutation_site
sample_outcome_prob     sample_outcome_prob
score_simulation        score_simulation
sim_seqdata             sim_seqdata
simulate                Generic function for simulate
simulate,lineage_tree_config,missing-method
                        simulate
simulate,lineage_tree_config,phyDat-method
                        simulate
simulate_core           simulate_core
substr_kmer             Generic function for substr_kmer
substr_kmer,kmer_summary-method
                        Subseting a kmer_summary object
subtract                Generic function for subtract
subtract,lineage_tree,lineage_tree-method
                        subtract
subtree                 Generic function for subtree
subtree,lineage_tree-method
                        subtree
subtree,phylo-method    subtree
summarize_kmer          Generic function for summarize_kmer
summarize_kmer,phyDat-method
                        summarize_kmer
summarize_kmer_core     summarize_kmer_core
