Files in jakubkala/QuiPTsim

R/QuiPTevaluation.R R/benchmark.R R/benchmark_ranking.R R/benchmark_utils.R R/cosine_similarity.R R/create_simulation_data.R R/create_simulation_data_setOfMotifs.R R/generate_sequences.R R/metrics.R R/ngram_probs.R R/results_analysis.R README.md inst/AmylogramExp - prepare data.R inst/QuiPT_sequence_generation.R inst/QuiPT_sequence_generation_exp3_15motifs.R inst/QuiPT_sequence_generation_exp3_5motifs.R inst/QuiPT_sequence_generation_reduced_alph.R inst/QuiPT_simulation_summary.R inst/QuiPTdiagramme.R inst/add_unigrams.R inst/amylogram_exp_analysis.R inst/encodings.R inst/experiments-results-summary.R inst/experiments/add_unigrams.R inst/experiments/exp-03-15motifs/exp03_nSeq300_nMotifs1_frac01.R inst/experiments/exp-03-15motifs/exp03_nSeq300_nMotifs1_frac025.R inst/experiments/exp-03-15motifs/exp03_nSeq300_nMotifs1_frac05.R inst/experiments/exp-03-15motifs/exp03_nSeq300_nMotifs1_frac075.R inst/experiments/exp-03-15motifs/exp03_nSeq300_nMotifs1_frac09.R inst/experiments/exp-03-15motifs/exp03_nSeq300_nMotifs2_frac01.R inst/experiments/exp-03-15motifs/exp03_nSeq300_nMotifs2_frac025.R inst/experiments/exp-03-15motifs/exp03_nSeq300_nMotifs2_frac05.R inst/experiments/exp-03-15motifs/exp03_nSeq300_nMotifs2_frac075.R inst/experiments/exp-03-15motifs/exp03_nSeq300_nMotifs2_frac09.R inst/experiments/exp-03-15motifs/exp03_nSeq600_nMotifs1_frac01.R inst/experiments/exp-03-15motifs/exp03_nSeq600_nMotifs1_frac025.R inst/experiments/exp-03-15motifs/exp03_nSeq600_nMotifs1_frac05.R inst/experiments/exp-03-15motifs/exp03_nSeq600_nMotifs1_frac075.R inst/experiments/exp-03-15motifs/exp03_nSeq600_nMotifs1_frac09.R inst/experiments/exp-03-15motifs/exp03_nSeq600_nMotifs2_frac01.R inst/experiments/exp-03-15motifs/exp03_nSeq600_nMotifs2_frac025.R inst/experiments/exp-03-15motifs/exp03_nSeq600_nMotifs2_frac05.R inst/experiments/exp-03-15motifs/exp03_nSeq600_nMotifs2_frac075.R inst/experiments/exp-03-15motifs/exp03_nSeq600_nMotifs2_frac09.R inst/experiments/exp-03-5motifs/exp03_nSeq300_nMotifs1_frac01.R inst/experiments/exp-03-5motifs/exp03_nSeq300_nMotifs1_frac025.R inst/experiments/exp-03-5motifs/exp03_nSeq300_nMotifs1_frac05.R inst/experiments/exp-03-5motifs/exp03_nSeq300_nMotifs1_frac075.R inst/experiments/exp-03-5motifs/exp03_nSeq300_nMotifs1_frac09.R inst/experiments/exp-03-5motifs/exp03_nSeq300_nMotifs2_frac01.R inst/experiments/exp-03-5motifs/exp03_nSeq300_nMotifs2_frac025.R inst/experiments/exp-03-5motifs/exp03_nSeq300_nMotifs2_frac05.R inst/experiments/exp-03-5motifs/exp03_nSeq300_nMotifs2_frac075.R inst/experiments/exp-03-5motifs/exp03_nSeq300_nMotifs2_frac09.R inst/experiments/exp-03-5motifs/exp03_nSeq600_nMotifs1_frac01.R inst/experiments/exp-03-5motifs/exp03_nSeq600_nMotifs1_frac025.R inst/experiments/exp-03-5motifs/exp03_nSeq600_nMotifs1_frac05.R inst/experiments/exp-03-5motifs/exp03_nSeq600_nMotifs1_frac075.R inst/experiments/exp-03-5motifs/exp03_nSeq600_nMotifs1_frac09.R inst/experiments/exp-03-5motifs/exp03_nSeq600_nMotifs2_frac01.R inst/experiments/exp-03-5motifs/exp03_nSeq600_nMotifs2_frac025.R inst/experiments/exp-03-5motifs/exp03_nSeq600_nMotifs2_frac05.R inst/experiments/exp-03-5motifs/exp03_nSeq600_nMotifs2_frac075.R inst/experiments/exp-03-5motifs/exp03_nSeq600_nMotifs2_frac09.R inst/experiments/exp-03/exp03_nSeq300_nMotifs1_frac01.R inst/experiments/exp-03/exp03_nSeq300_nMotifs1_frac025.R inst/experiments/exp-03/exp03_nSeq300_nMotifs1_frac05.R inst/experiments/exp-03/exp03_nSeq300_nMotifs1_frac075.R inst/experiments/exp-03/exp03_nSeq300_nMotifs1_frac09.R inst/experiments/exp-03/exp03_nSeq300_nMotifs2_frac01.R inst/experiments/exp-03/exp03_nSeq300_nMotifs2_frac025.R inst/experiments/exp-03/exp03_nSeq300_nMotifs2_frac05.R inst/experiments/exp-03/exp03_nSeq300_nMotifs2_frac075.R inst/experiments/exp-03/exp03_nSeq300_nMotifs2_frac09.R inst/experiments/exp-03/exp03_nSeq600_nMotifs1_frac01.R inst/experiments/exp-03/exp03_nSeq600_nMotifs1_frac025.R inst/experiments/exp-03/exp03_nSeq600_nMotifs1_frac05.R inst/experiments/exp-03/exp03_nSeq600_nMotifs1_frac075.R inst/experiments/exp-03/exp03_nSeq600_nMotifs1_frac09.R inst/experiments/exp-03/exp03_nSeq600_nMotifs2_frac01.R inst/experiments/exp-03/exp03_nSeq600_nMotifs2_frac025.R inst/experiments/exp-03/exp03_nSeq600_nMotifs2_frac05.R inst/experiments/exp-03/exp03_nSeq600_nMotifs2_frac075.R inst/experiments/exp-03/exp03_nSeq600_nMotifs2_frac09.R inst/experiments/exp01_seqLen10_nSeq300_amylogram_encoding.R inst/experiments/exp01_seqLen10_nSeq300_amylogram_encoding_infogain.R inst/experiments/exp01_seqLen10_nSeq300_frac01_amylogram_encoding.R inst/experiments/exp01_seqLen10_nSeq300_frac025_amylogram_encoding.R inst/experiments/exp01_seqLen10_nSeq300_frac075_amylogram_encoding.R inst/experiments/exp01_seqLen10_nSeq300_frac09_amylogram_encoding.R inst/experiments/exp01_seqLen10_nSeq600_frac01_amylogram_encoding.R inst/experiments/exp01_seqLen10_nSeq600_frac025_amylogram_encoding.R inst/experiments/exp01_seqLen10_nSeq600_frac075_amylogram_encoding.R inst/experiments/exp01_seqLen10_nSeq600_frac09_amylogram_encoding.R inst/plan.R inst/plots-kmer-dimensionality.R inst/presentation-followup.Rmd inst/presentation.Rmd inst/ranking.R inst/ranking_example.R inst/run_benchmark.R inst/run_simulation_example.R inst/su_comparison.R inst/unbalanced-experiments.R man/F1score.Rd man/QuiPTsimBenchmark.Rd man/accuracy.Rd man/add_motifs.Rd man/aggregate_metrics.Rd man/aggregate_results.Rd man/benchmark_summary.Rd man/build_model.Rd man/calculate_ngram_prob.Rd man/calculate_score.Rd man/calculate_seq_prob.Rd man/collect_filtering_times.Rd man/compute_metrics.Rd man/cosine_similarity.Rd man/count_ngrams.Rd man/create_benchmark_data.Rd man/create_simulation_data.Rd man/create_simulation_data_set_of_motifs.Rd man/euclidean_norm.Rd man/evaluate_filtering_results.Rd man/evaluate_models.Rd man/evaluate_selected_kmers.Rd man/filter_ngrams.Rd man/filter_nonrankings.Rd man/filter_nonrankings_exp3.Rd man/filter_rankings.Rd man/filter_rankings_exp3.Rd man/generate_motifs.Rd man/generate_probs.Rd man/generate_sequences.Rd man/generate_single_motif.Rd man/kmers_for_nonranking_methods.Rd man/parse_results.Rd man/positive_ngrams.Rd man/precision.Rd man/rbind_ngram_matrices.Rd man/rbind_ngrams.Rd man/read_ngram_matrix.Rd man/read_simulation_data.Rd man/recall.Rd man/sensitivity.Rd man/sequenceTransitionMatrix.Rd man/simulate_sequences.Rd man/simulate_single_sequence.Rd man/specificity.Rd man/subset_matrix.Rd man/validate_motifs.Rd renv/activate.R tests/spelling.R tests/testthat.R tests/testthat/test_QuiPTevaluation.R tests/testthat/test_benchmark.R tests/testthat/test_benchmark_ranking.R tests/testthat/test_cosine_similarity.R tests/testthat/test_create_simulation_data.R tests/testthat/test_generate_sequences.R tests/testthat/test_ngram_probs.R vignettes/QuiPTsimDescription.Rmd vignettes/experiments-results-summary.Rmd vignettes/methods-for-k-mers-filtering.Rmd vignettes/unbalanced_experiments.Rmd vignettes/vignette.Rmd