Index Symbols | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | V | W Symbols --bounding scphylo-solver-bnb command line option --experiment scphylo-solver-scite command line option --n_iterations scphylo-solver-booster command line option --n_iters scphylo-solver-scite command line option --n_jobs scphylo-solver-booster command line option --n_restarts scphylo-solver-scite command line option --n_samples scphylo-solver-booster command line option scphylo-utils-partf command line option --n_threads scphylo-solver-scite command line option scphylo-utils-partf command line option --processes scphylo-utils-search command line option --sample_size scphylo-solver-booster command line option --seed scphylo-solver-scite command line option --solver scphylo-solver-booster command line option --version scphylo command line option -b scphylo-solver-bnb command line option -e scphylo-solver-scite command line option -l scphylo-solver-scite command line option -p scphylo-utils-search command line option -r scphylo-solver-scite command line option -s scphylo-solver-scite command line option -t scphylo-solver-scite command line option A acute_lymphocytic_leukemia1() (in module scphylo.datasets) acute_lymphocytic_leukemia2() (in module scphylo.datasets) acute_lymphocytic_leukemia3() (in module scphylo.datasets) acute_lymphocytic_leukemia4() (in module scphylo.datasets) acute_lymphocytic_leukemia5() (in module scphylo.datasets) acute_lymphocytic_leukemia6() (in module scphylo.datasets) acute_myeloid_leukemia1() (in module scphylo.datasets) acute_myeloid_leukemia2() (in module scphylo.datasets) acute_myeloid_leukemia_many() (in module scphylo.datasets) ad() (in module scphylo.tl) adata (scphylo.pp.filter_mut_mutant_must_present_in_at_least parameter), [1] (scphylo.pp.filter_mut_reference_must_present_in_at_least parameter), [1] (scphylo.pp.remove_cell_by_list parameter), [1] (scphylo.pp.remove_mut_by_list parameter), [1] add_noise() (in module scphylo.datasets) add_readcount() (in module scphylo.datasets) alist (scphylo.pp.remove_cell_by_list parameter), [1] (scphylo.pp.remove_mut_by_list parameter), [1] ALPHA scphylo-solver-booster command line option scphylo-solver-huntress command line option scphylo-solver-phiscsb command line option scphylo-solver-scistree command line option scphylo-solver-scite command line option scphylo-utils-partf command line option alpha (scphylo.datasets.add_noise parameter), [1] (scphylo.datasets.simulate parameter), [1] (scphylo.tl.booster parameter), [1] (scphylo.tl.gpps parameter), [1] (scphylo.tl.huntress parameter), [1] (scphylo.tl.onconem parameter), [1] (scphylo.tl.partition_function parameter), [1] (scphylo.tl.phiscsb parameter), [1] (scphylo.tl.phiscsi_bulk parameter), [1] (scphylo.tl.scistree parameter), [1] (scphylo.tl.scite parameter), [1] (scphylo.tl.siclonefit parameter), [1] (scphylo.tl.sphyr parameter), [1] annotation (scphylo.pl.dendro_tree parameter), [1] B begin_index (scphylo.tl.booster parameter), [1] BETA scphylo-solver-booster command line option scphylo-solver-huntress command line option scphylo-solver-phiscsb command line option scphylo-solver-scistree command line option scphylo-solver-scite command line option scphylo-utils-partf command line option beta (scphylo.datasets.add_noise parameter), [1] (scphylo.datasets.simulate parameter), [1] (scphylo.tl.booster parameter), [1] (scphylo.tl.gpps parameter), [1] (scphylo.tl.huntress parameter), [1] (scphylo.tl.onconem parameter), [1] (scphylo.tl.partition_function parameter), [1] (scphylo.tl.phiscsb parameter), [1] (scphylo.tl.phiscsi_bulk parameter), [1] (scphylo.tl.scistree parameter), [1] (scphylo.tl.scite parameter), [1] (scphylo.tl.siclonefit parameter), [1] (scphylo.tl.sphyr parameter), [1] bifiltering() (in module scphylo.pp) bnb() (in module scphylo.tl) booster() (in module scphylo.tl) bounding (scphylo.tl.bnb parameter), [1] C caset() (in module scphylo.tl) cell_info (scphylo.pl.clonal_tree parameter), [1] (scphylo.pl.dendro_tree parameter), [1] cellr (scphylo.pp.bifiltering parameter), [1] cells (scphylo.tl.partition_function parameter), [1] cells_as_number (scphylo.pl.clonal_tree parameter), [1] clonal_tree() (in module scphylo.pl) color_attr (scphylo.pl.clonal_tree parameter), [1] colorectal1() (in module scphylo.datasets) colorectal2() (in module scphylo.datasets) colorectal3() (in module scphylo.datasets) comm (scphylo.tl.bnb parameter), [1] consensus() (in module scphylo.tl) consensus_combine() (in module scphylo.pp) D DATA scphylo-solver-bnb command line option scphylo-solver-booster command line option scphylo-solver-huntress command line option scphylo-solver-phiscsb command line option scphylo-solver-scistree command line option scphylo-solver-scite command line option delta (scphylo.tl.phiscsi_bulk parameter), [1] dendro_tree() (in module scphylo.pl) dep_weight (scphylo.tl.booster parameter), [1] df (scphylo.pp.bifiltering parameter), [1] (scphylo.pp.consensus_combine parameter), [1] (scphylo.ul.hclustering parameter), [1] (scphylo.ul.to_tree parameter), [1] df1 (scphylo.tl.consensus parameter), [1] df2 (scphylo.tl.consensus parameter), [1] df_grnd (scphylo.tl.ad parameter), [1] (scphylo.tl.caset parameter), [1] (scphylo.tl.disc parameter), [1] (scphylo.tl.dl parameter), [1] (scphylo.tl.gs parameter), [1] (scphylo.tl.mltd parameter), [1] (scphylo.tl.mp3 parameter), [1] (scphylo.tl.rf parameter), [1] (scphylo.tl.tpted parameter), [1] df_in (scphylo.datasets.add_noise parameter), [1] (scphylo.datasets.add_readcount parameter), [1] (scphylo.ul.is_conflict_free parameter), [1] (scphylo.ul.is_conflict_free_gusfield parameter), [1] df_input (scphylo.tl.bnb parameter), [1] (scphylo.tl.booster parameter), [1] (scphylo.tl.gpps parameter), [1] (scphylo.tl.huntress parameter), [1] (scphylo.tl.onconem parameter), [1] (scphylo.tl.partition_function parameter), [1] (scphylo.tl.phiscsb parameter), [1] (scphylo.tl.phiscsi_bulk parameter), [1] (scphylo.tl.scelestial parameter), [1] (scphylo.tl.scistree parameter), [1] (scphylo.tl.scite parameter), [1] (scphylo.tl.siclonefit parameter), [1] (scphylo.tl.sphyr parameter), [1] df_sol (scphylo.tl.ad parameter), [1] (scphylo.tl.caset parameter), [1] (scphylo.tl.disc parameter), [1] (scphylo.tl.dl parameter), [1] (scphylo.tl.gs parameter), [1] (scphylo.tl.mltd parameter), [1] (scphylo.tl.mp3 parameter), [1] (scphylo.tl.rf parameter), [1] (scphylo.tl.tpted parameter), [1] disable_tqdm (scphylo.tl.booster parameter), [1] disc() (in module scphylo.tl) distance_labels_to_bottom (scphylo.pl.dendro_tree parameter), [1] dl() (in module scphylo.tl) dpi (scphylo.pl.clonal_tree parameter), [1] (scphylo.pl.dendro_tree parameter), [1] E erbc() (in module scphylo.datasets) example() (in module scphylo.datasets) executable (scphylo.tl.sphyr parameter), [1] experiment (scphylo.tl.phiscsb parameter), [1] (scphylo.tl.scistree parameter), [1] (scphylo.tl.scite parameter), [1] (scphylo.tl.siclonefit parameter), [1] F FILE scphylo-utils-cf2newick command line option scphylo-utils-cf2tree command line option scphylo-utils-search command line option FILE1 scphylo-utils-consensus command line option scphylo-utils-score command line option FILE2 scphylo-utils-consensus command line option scphylo-utils-score command line option filepath (scphylo.io.read parameter), [1] (scphylo.io.write parameter), [1] filter_mut_mutant_must_present_in_at_least() (in module scphylo.pp) filter_mut_reference_must_present_in_at_least() (in module scphylo.pp) G GENOTYPE_FILE scphylo-utils-partf command line option gpps() (in module scphylo.tl) gs() (in module scphylo.tl) H hclustering() (in module scphylo.ul) height (scphylo.pl.dendro_tree parameter), [1] high_grade_serous_ovarian_cancer1() (in module scphylo.datasets) high_grade_serous_ovarian_cancer2() (in module scphylo.datasets) high_grade_serous_ovarian_cancer3() (in module scphylo.datasets) high_grade_serous_ovarian_cancer_3celllines() (in module scphylo.datasets) huntress() (in module scphylo.tl) I inner_node_size (scphylo.pl.dendro_tree parameter), [1] inner_node_type (scphylo.pl.dendro_tree parameter), [1] instance (scphylo.datasets.acute_myeloid_leukemia_many parameter), [1] is_conflict_free() (in module scphylo.ul) is_conflict_free_gusfield() (in module scphylo.ul) isogenic_fibroblast_cell_line() (in module scphylo.datasets) J jar_path (scphylo.tl.siclonefit parameter), [1] java_executable (scphylo.tl.siclonefit parameter), [1] K k_dollo (scphylo.tl.gpps parameter), [1] kmax (scphylo.tl.phiscsi_bulk parameter), [1] L label_color (scphylo.pl.dendro_tree parameter), [1] line_size (scphylo.pl.dendro_tree parameter), [1] M max_del (scphylo.tl.gpps parameter), [1] mean_coverage (scphylo.datasets.add_readcount parameter), [1] melanoma20() (in module scphylo.datasets) method (scphylo.ul.hclustering parameter), [1] metric (scphylo.ul.hclustering parameter), [1] min_cells (scphylo.pp.filter_mut_mutant_must_present_in_at_least parameter), [1] (scphylo.pp.filter_mut_reference_must_present_in_at_least parameter), [1] missing (scphylo.datasets.add_noise parameter), [1] (scphylo.datasets.simulate parameter), [1] mltd() (in module scphylo.tl) module scphylo scphylo.datasets scphylo.io scphylo.pl scphylo.pp scphylo.tl scphylo.ul mp3() (in module scphylo.tl) muscle_invasive_bladder() (in module scphylo.datasets) mutr (scphylo.pp.bifiltering parameter), [1] muts (scphylo.tl.partition_function parameter), [1] muts_as_number (scphylo.pl.clonal_tree parameter), [1] myeloproliferative_neoplasms18() (in module scphylo.datasets) myeloproliferative_neoplasms712() (in module scphylo.datasets) myeloproliferative_neoplasms78() (in module scphylo.datasets) N n_batches (scphylo.tl.partition_function parameter), [1] n_burnin (scphylo.tl.siclonefit parameter), [1] n_cell_clusters (scphylo.tl.sphyr parameter), [1] n_cells (scphylo.datasets.simulate parameter), [1] n_clones (scphylo.datasets.simulate parameter), [1] n_iterations (scphylo.tl.booster parameter), [1] n_iters (scphylo.tl.gpps parameter), [1] (scphylo.tl.scite parameter), [1] (scphylo.tl.siclonefit parameter), [1] n_jobs (scphylo.tl.booster parameter), [1] n_mut_clusters (scphylo.tl.sphyr parameter), [1] n_muts (scphylo.datasets.simulate parameter), [1] n_restarts (scphylo.tl.scite parameter), [1] (scphylo.tl.siclonefit parameter), [1] (scphylo.tl.sphyr parameter), [1] n_samples (scphylo.tl.booster parameter), [1] (scphylo.tl.partition_function parameter), [1] n_threads (scphylo.tl.gpps parameter), [1] (scphylo.tl.huntress parameter), [1] (scphylo.tl.phiscsi_bulk parameter), [1] (scphylo.tl.scistree parameter), [1] (scphylo.tl.sphyr parameter), [1] neighbor_size (scphylo.tl.gpps parameter), [1] no_dependencies (scphylo.tl.booster parameter), [1] no_reconstruction (scphylo.tl.booster parameter), [1] no_subsampling (scphylo.tl.booster parameter), [1] O obj (scphylo.io.write parameter), [1] onconem() (in module scphylo.tl) OUTPUT scphylo-utils-consensus command line option output_file (scphylo.pl.clonal_tree parameter), [1] (scphylo.pl.dendro_tree parameter), [1] P partition_function() (in module scphylo.tl) phiscsb() (in module scphylo.tl) phiscsi_bulk() (in module scphylo.tl) R read() (in module scphylo.io) readcount (scphylo.datasets.colorectal2 parameter), [1] remove_cell_by_list() (in module scphylo.pp) remove_mut_by_list() (in module scphylo.pp) renal_cell_carcinoma() (in module scphylo.datasets) return_tree (scphylo.tl.siclonefit parameter), [1] rf() (in module scphylo.tl) ruby_executable (scphylo.tl.gpps parameter), [1] S sample_on (scphylo.tl.booster parameter), [1] sample_size (scphylo.tl.booster parameter), [1] scelestial() (in module scphylo.tl) scistree() (in module scphylo.tl) scite() (in module scphylo.tl) scphylo module scphylo command line option --version scphylo-solver-bnb command line option --bounding -b DATA scphylo-solver-booster command line option --n_iterations --n_jobs --n_samples --sample_size --solver ALPHA BETA DATA scphylo-solver-huntress command line option ALPHA BETA DATA scphylo-solver-phiscsb command line option ALPHA BETA DATA scphylo-solver-scistree command line option ALPHA BETA DATA scphylo-solver-scite command line option --experiment --n_iters --n_restarts --n_threads --seed -e -l -r -s -t ALPHA BETA DATA scphylo-utils-cf2newick command line option FILE scphylo-utils-cf2tree command line option FILE scphylo-utils-consensus command line option FILE1 FILE2 OUTPUT scphylo-utils-partf command line option --n_samples --n_threads ALPHA BETA GENOTYPE_FILE scphylo-utils-score command line option FILE1 FILE2 scphylo-utils-search command line option --processes -p FILE scphylo.datasets module scphylo.io module scphylo.pl module scphylo.pp module scphylo.tl module scphylo.ul module seed (scphylo.datasets.add_readcount parameter), [1] show (scphylo.pl.clonal_tree parameter), [1] (scphylo.pl.dendro_tree parameter), [1] show_id (scphylo.pl.clonal_tree parameter), [1] siclonefit() (in module scphylo.tl) simulate() (in module scphylo.datasets) solver (scphylo.tl.booster parameter), [1] sphyr() (in module scphylo.tl) subsample_dir (scphylo.tl.booster parameter), [1] T time_limit (scphylo.pp.bifiltering parameter), [1] (scphylo.tl.bnb parameter), [1] (scphylo.tl.booster parameter), [1] (scphylo.tl.gpps parameter), [1] (scphylo.tl.phiscsi_bulk parameter), [1] (scphylo.tl.sphyr parameter), [1] tiplab_size (scphylo.pl.dendro_tree parameter), [1] tnbc() (in module scphylo.datasets) to_cfmatrix() (in module scphylo.ul) to_mtree() (in module scphylo.ul) to_tree() (in module scphylo.ul) tools_dir (scphylo.tl.gpps parameter), [1] (scphylo.tl.siclonefit parameter), [1] (scphylo.tl.sphyr parameter), [1] tpted() (in module scphylo.tl) tree (scphylo.pl.clonal_tree parameter), [1] (scphylo.pl.dendro_tree parameter), [1] (scphylo.ul.to_cfmatrix parameter), [1] (scphylo.ul.to_mtree parameter), [1] tree_script (scphylo.tl.gpps parameter), [1] V vaf_info (scphylo.tl.phiscsi_bulk parameter), [1] W width (scphylo.pl.dendro_tree parameter), [1] write() (in module scphylo.io)
