Files in Kalhor-Lab/QFM
Quantitative Fate Mapping with ICE-FASE and Phylotime

.Rbuildignore

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DESCRIPTION

LICENSE

NAMESPACE

R/backward_sample.R R/deprecated.R R/evaulate_experiment.R R/exp_pipeline.R R/graph_construction.R R/ice_fase.R R/ice_fase_evaluate.R

R/ice_fase_mod1.R

R/ice_fase_multifurc.R R/impute_character_matrix.R R/multi_replicates.R R/mutation.R R/mutation_matrix.R R/phylogeny_likelihood.R R/phylogeny_model.R R/phylogeny_model_v2.R R/phylotime.R R/plotting.R R/process_single_cell.R R/read_id_spacer.R R/simulation_func.R R/single_cell_barcode.R R/test_func.R R/tree_data_io.R R/tree_utils.R R/type_graph.R R/utils.R README.md

_pkgdown.yml

analysis/MARC1_estimation/MARC1_estimation_func.R analysis/MARC1_estimation/README.md analysis/MARC1_estimation/analyze_MARC1.R analysis/MARC1_estimation/load_MARC1_data.R analysis/MARC1_estimation/sample_MARC1_hgRNA.R analysis/README.md

analysis/extended_experiments/README.html

analysis/main_panel/README.html

analysis/main_panel/README.md analysis/main_panel/benchmark_phylotime.R analysis/main_panel/construct_fate_map_panel.R analysis/main_panel/evaluate_ice_fase_phylotime.R analysis/main_panel/figure1.R analysis/main_panel/figure2and3.R analysis/main_panel/make_example_data.R analysis/main_panel/setup_experiments.R analysis/main_panel/simulate_process_evaluate.R analysis/main_panel/slurm_phylotime_data.R analysis/main_panel/slurm_phylotime_varying_sites.R analysis/main_panel/slurm_processing.R analysis/splitwell_experiment/README.md analysis/splitwell_experiment/compare_splitwell.R analysis/splitwell_experiment/process_splitwell.R analysis/splitwell_experiment/simulate_splitwell.R

data/example/MARC1_id_prob.rds

data/example/MARC1_indelphi_predicted.rds

data/example/cell_type.csv

data/example/mut_p_marc1.rds

data/example/mut_p_mut_rate.csv

data/example/mut_p_recur_vec.csv

data/example/mutant_allele_matrix.csv

data/example/mutant_allele_matrix_with_missing.csv

data/example/tree.txt

data/example/tree_panel.rds

doc/basic_tutorial.R doc/basic_tutorial.Rmd

doc/basic_tutorial.html

docs/._index.html

docs/404.html

docs/LICENSE-text.html

docs/articles/basic_tutorial.html

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docs/articles/operations.html

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docs/authors.html

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docs/reference/calc_bsum.html

docs/reference/calculate_type_counts.html

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docs/reference/check_n_identity.html

docs/reference/collaspe_di.html

docs/reference/concat_mut_p.html

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docs/reference/distribute_mut_counts.html

docs/reference/edges_df_to_newick.html

docs/reference/generate_diff_outcome.html

docs/reference/generate_edge_df.html

docs/reference/generate_mut_ids.html

docs/reference/generate_nonrecur_mut_ids.html

docs/reference/generate_recur_mut_ids.html

docs/reference/get_cell_type_counts.html

docs/reference/get_edge_diff.html

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docs/reference/get_mut_duration.html

docs/reference/get_next.html

docs/reference/get_node_mapping.html

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docs/reference/get_sampled_cells.html

docs/reference/get_t_total.html

docs/reference/get_target_time.html

docs/reference/get_true_size_mod2.html

docs/reference/hello.html

docs/reference/ice_fase.html

docs/reference/impute_characters.html

docs/reference/index.html

docs/reference/init_mut_counts_list.html

docs/reference/initial_states_list.html

docs/reference/initialize_mut_element_counter.html

docs/reference/initialize_mut_state.html

docs/reference/is_non_decs.html

docs/reference/is_zero_range.html

docs/reference/make_gr_tr_data.html

docs/reference/make_heatmap_col.html

docs/reference/make_mut_element.html

docs/reference/make_mut_param_by_rate.html

docs/reference/make_mut_param_by_rate_rvec.html

docs/reference/make_type_graph.html

docs/reference/mut_counts_total.html

docs/reference/mutate_barcodes.html

docs/reference/mutate_cells.html

docs/reference/normalize_row.html

docs/reference/normalize_tree.html

docs/reference/num_gen_single_type.html

docs/reference/phylotime.html

docs/reference/plot_col_vec.html

docs/reference/plot_gr_data.html

docs/reference/plot_legend.html

docs/reference/plot_type_graph.html

docs/reference/push_pdf.html

docs/reference/push_png.html

docs/reference/rstoc.html

docs/reference/sample_all_mut_counts.html

docs/reference/sample_all_mut_counts_gen.html

docs/reference/sample_doublet_branch.html

docs/reference/sample_doublet_twotype.html

docs/reference/sample_mut_counts.html

docs/reference/scale_counts.html

docs/reference/sim_history_to_edges.html

docs/reference/sim_history_to_nodes.html

docs/reference/simplify_edges_df.html

docs/reference/subsample_all_mut_counts.html

docs/reference/subsample_mut_counts.html

docs/reference/subset_mut_p.html

docs/reference/white_col_mapper.html

docs/search.json

docs/sitemap.xml

man/add_edge_length.Rd man/as.phylo.type_graph.Rd man/calc_bsum.Rd man/calculate_type_counts.Rd man/cells_to_edges.Rd man/cells_to_nodes.Rd man/change_target_time.Rd man/check_n_identity.Rd man/collaspe_di.Rd man/concat_mut_p.Rd man/concat_mut_p_list.Rd man/construct_true_lineage_multi.Rd man/distribute_all_mut_counts.Rd man/distribute_mut_counts.Rd man/edges_df_to_newick.Rd man/generate_diff_outcome.Rd man/generate_edge_df.Rd man/generate_mut_ids.Rd man/generate_nonrecur_mut_ids.Rd man/generate_recur_mut_ids.Rd man/get_cell_type_counts.Rd man/get_edge_diff.Rd man/get_edge_len.Rd man/get_mut_duration.Rd man/get_next.Rd man/get_node_mapping.Rd man/get_sample_size.Rd man/get_sampled_cells.Rd man/get_t_total.Rd man/get_target_time.Rd man/get_true_size_mod2.Rd man/hello.Rd man/ice_fase.Rd man/impute_characters.Rd man/init_mut_counts_list.Rd man/initial_states_list.Rd man/initialize_mut_element_counter.Rd man/initialize_mut_state.Rd man/is_non_decs.Rd man/is_zero_range.Rd man/make_gr_tr_data.Rd man/make_heatmap_col.Rd man/make_mut_element.Rd man/make_mut_param_by_rate.Rd man/make_mut_param_by_rate_rvec.Rd man/make_type_graph.Rd man/mut_counts_total.Rd man/mutate_barcodes.Rd man/mutate_cells.Rd man/normalize_row.Rd man/normalize_tree.Rd man/num_gen_single_type.Rd man/phylotime.Rd man/plot_col_vec.Rd man/plot_gr_data.Rd man/plot_legend.Rd man/plot_type_graph.Rd man/push_pdf.Rd man/push_png.Rd man/rstoc.Rd man/sample_all_mut_counts.Rd man/sample_all_mut_counts_gen.Rd man/sample_doublet_branch.Rd man/sample_doublet_twotype.Rd man/sample_mut_counts.Rd man/scale_counts.Rd man/sim_history_to_edges.Rd man/sim_history_to_nodes.Rd man/simplify_edges_df.Rd man/subsample_all_mut_counts.Rd man/subsample_mut_counts.Rd man/subset_mut_p.Rd man/white_col_mapper.Rd

metadata/MARC1/SupplementaryTable3 - TableS3-hgRNA Activities.csv

metadata/MARC1/TableS1.csv

qfm.Rproj

vignettes/.gitignore

vignettes/basic_tutorial.Rmd vignettes/operations.Rmd vignettes/simulate_phylogeny_and_barcodes.Rmd

Kalhor-Lab/QFM documentation built on Nov. 25, 2024, 10:18 p.m.

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Kalhor-Lab/QFM
Quantitative Fate Mapping with ICE-FASE and Phylotime

Files in Kalhor-Lab/QFM
Quantitative Fate Mapping with ICE-FASE and Phylotime

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Kalhor-Lab/QFM Quantitative Fate Mapping with ICE-FASE and Phylotime

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Kalhor-Lab/QFM
Quantitative Fate Mapping with ICE-FASE and Phylotime

Files in Kalhor-Lab/QFM
Quantitative Fate Mapping with ICE-FASE and Phylotime