Files in sams25/rcombinator_old
Tools to Simulate the Evolution of Genetic Sequences
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/burst_copies.R
R/choose_pairing.R
R/compare_all.R
R/compare_all_old.R
R/convert_init_dist_to_df.R
R/copy_number_evolution.R
R/copy_number_growth.R
R/cumulate_distribution.R
R/cumulate_matrix.R
R/dist_to_data_frame.R
R/find_parameter_balance_copy_number_variation.R
R/full_pipeline_comparison.R
R/get_distance_to_initial_timestep.R
R/get_k80_matrix.R
R/get_random_sequence.R
R/get_summary_stats.R
R/get_summary_stats_timestep.R
R/kill_copies.R
R/normalise_distribution.R
R/output_helpers.R
R/pairwise_distances.R
R/pairwise_distances_bursts.R
R/pairwise_distances_timestamp.R
R/pick_random_event.R
R/plot_pairwise_data.R
R/plot_pairwise_data_complex.R
R/plot_sequence_counts.R
R/plot_summary_stats.R
R/plot_summary_stats_complex.R
R/point_mutations.R
R/rcombinator.R
R/recombine_sequences.R
R/retrotransposon_evolution.R
R/simulate_burst_evolution.R
R/simulate_bursts.R
R/simulate_pairwise_distances_cheap.R
R/simulate_point_mutation_markov.R
R/simulate_point_mutation_markov_cheap.R
R/simulate_point_mutation_markov_expensive.R
R/simulate_recombination.R
R/simulate_recombination_cheap.R
R/simulate_recombination_expensive.R
R/simulate_recombination_families.R
R/simulate_recombination_summary.R
R/simulate_without_recombination.R
R/simulate_without_recombination_cheap.R
R/simulate_without_recombination_expensive.R
R/simulate_without_recombination_families.R
R/simulate_without_recombination_summary.R
R/stringdist_ape.R
R/stringdist_biostrings.R
R/stringdist_levenshtein.R
R/sysdata.rda
R/test_event.R
R/update_burst_mean.R
R/valid_ranges.R
README.md
compare_stats_families.R
compare_stats_global.R
cpp/Makefile
cpp/analyse_output/analyse_output.R
cpp/analyse_output/header.R
cpp/analyse_output/values.R
cpp/constants.hpp
cpp/io.hpp
cpp/main.cpp
cpp/main_no_bursts.cpp
cpp/main_with_flags.cpp
cpp/main_without_flags.cpp
cpp/math_helpers.hpp
cpp/output/0.1_500_100_0.05_0.5_0.001.csv
cpp/output/0.1_500_100_0.05_0.5_0.001.in
cpp/output/0.1_500_100_0.05_0.5_0.1.csv
cpp/output/0.1_500_100_0.05_0.5_0.1.in
cpp/output/0.1_500_100_0.05_0.5_1.0.csv
cpp/output/0.1_500_100_0.05_0.5_1.0.in
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cpp/output/0.1_500_100_0.05_1_0.001.in
cpp/output/0.1_500_100_0.05_1_0.1.csv
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cpp/output/base_input.in_use
cpp/output/create_input_files.py
cpp/output/dummy_input.in_use
cpp/output/run_scan_1.sh
cpp/output/run_scan_2.sh
cpp/output_gene/base_input.in_use
cpp/output_gene/dummy_input.in_use
cpp/output_gene/dummy_output.csv
cpp/output_gene/gene_0.1_250_20_10.in
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cpp/output_gene/parameter_scan.py
cpp/output_pair/base_input.in_use
cpp/output_pair/dummy_input_with.in_use
cpp/output_pair/dummy_input_without.in_use
cpp/output_pair/parameter_scan.py
cpp/output_pair/run_dummy.sh
cpp/output_pair/run_scan_1.sh
cpp/output_pair/run_scan_2.sh
cpp/output_pair/run_scan_3.sh
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data-raw/NUCLEOTIDES.R
full_pipeline_new.R
man/burst_copies.Rd
man/choose_pairing.Rd
man/compare_all.Rd
man/convert_init_dist_to_df.Rd
man/copy_number_evolution.Rd
man/copy_number_growth.Rd
man/cumulate_distribution.Rd
man/cumulate_matrix.Rd
man/dist_to_data_frame.Rd
man/find_paramater_balance_copy_number_variation.Rd
man/full_pipeline_comparison.Rd
man/get_distance_to_initial_timestep.Rd
man/get_k80_matrix.Rd
man/get_random_sequence.Rd
man/get_summary_stats.Rd
man/get_summary_stats_timestep.Rd
man/kill_copies.Rd
man/normalise_distribution.Rd
man/pairwise_distances.Rd
man/pairwise_distances_bursts.Rd
man/pairwise_distances_timestamp.Rd
man/pick_random_event.Rd
man/plot_pairwise_data.Rd
man/plot_pairwise_data_complex.Rd
man/plot_sequence_counts.Rd
man/plot_summary_stats.Rd
man/plot_summary_stats_complex.Rd
man/point_mutation_nucleotide.Rd
man/point_mutation_sequence.Rd
man/point_mutation_sequences.Rd
man/rcombinator.Rd
man/recombine_sequences.Rd
man/retrotransposon_evolution.Rd
man/simulate_burst_evolution.Rd
man/simulate_bursts.Rd
man/simulate_point_mutation_markov.Rd
man/simulate_point_mutation_markov_cheap.Rd
man/simulate_point_mutation_markov_expensive.Rd
man/simulate_recombination.Rd
man/simulate_recombination_cheap.Rd
man/simulate_recombination_expensive.Rd
man/simulate_recombination_families.Rd
man/simulate_recombination_summary.Rd
man/simulate_without_recombination.Rd
man/simulate_without_recombination_cheap.Rd
man/simulate_without_recombination_expensive.Rd
man/simulate_without_recombination_families.Rd
man/simulate_without_recombination_summary.Rd
man/stringdist_ape.Rd
man/stringdist_biostrings.Rd
man/stringdist_levenshtein.Rd
man/test_event.Rd
man/update_burst_mean.Rd
man/valid_ranges.Rd
rcombinator.Rproj
vignettes/Simulate_Burst_Events.Rmd
vignettes/Simulate_Point_Mutations.Rmd
vignettes/Simulate_Recombination.Rmd
