add_deletion |
add_deletion |
add_dropout |
add_dropout |
as_igraph |
Generic function for as_igraph |
as_igraph-method |
as_igraph |
as_igraph-method |
as_igraph |
as_lineage_tree |
Generic function for as_lineage_tree |
as_lineage_tree-method |
as_lineage_tree |
as_phylo |
Generic function for as_phylo |
as_phylo-method |
as_phylo |
DCLEAR |
DCLEAR: A package for DCLEAR: Distance based Cell LinEAge Reconstruction |
dist_kmer_replacement_inference |
Core function of computing kmer replacement distance |
dist_replacement |
Generic function for dist_replacement |
dist_replacement-method |
Compute the kmer replacement distance |
dist_replacement-method |
Compute the kmer replacement distance |
dist_weighted_hamming |
Generic function for dist_weighted_hamming |
dist_weighted_hamming-method |
dist_weighted_hamming |
downsample |
Generic function for downsample |
downsample-method |
downsample |
downsample-method |
downsample |
get_distance_prior |
get_distance_prior |
get_leaves |
Generic function for get_leaves |
get_leaves-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-method |
Process sequences |
prune |
Generic function for prune |
prune-method |
prune |
prune-method |
prune |
random_tree |
random_tree |
rbind-method |
rbind |
sample_mutation_outcome |
sample_mutation_outcome |
sample_mutation_site |
sample_mutation_site |
sample_outcome_prob |
sample_outcome_prob |
score_simulation |
score_simulation |
simulate |
Generic function for simulate |
simulate-method |
simulate |
simulate-method |
simulate |
simulate_core |
simulate_core |
sim_seqdata |
sim_seqdata |
substr_kmer |
Generic function for substr_kmer |
substr_kmer-method |
Subseting a kmer_summary object |
subtract |
Generic function for subtract |
subtract-method |
subtract |
subtree |
Generic function for subtree |
subtree-method |
subtree |
subtree-method |
subtree |
summarize_kmer |
Generic function for summarize_kmer |
summarize_kmer-method |
summarize_kmer |
summarize_kmer_core |
summarize_kmer_core |
WH |
WH |
WH_train |
Train weights for WH |
WH_train_fit |
Train weights for WH, and output distance object |