Man pages for lehner-lab/DiMSum
A pipeline for processing deep mutational scanning data
| dimsum | Run DiMSum pipeline |
| dimsum__aggregate_AA_variants | dimsum__aggregate_AA_variants |
| dimsum__aggregate_AA_variants_fitness | dimsum__aggregate_AA_variants_fitness |
| dimsum__bayesian_double_fitness | dimsum__bayesian_double_fitness |
| dimsum__calculate_fitness | dimsum__calculate_fitness |
| dimsum__cbind_fill | dimsum__cbind_fill |
| dimsum__check_barcode_design | dimsum__check_barcode_design |
| dimsum__check_barcodeidentityfile | dimsum__check_barcodeidentityfile |
| dimsum__check_countfile | dimsum__check_countfile |
| dimsum__check_experiment_design | dimsum__check_experiment_design |
| dimsum__check_experiment_design_countfile | dimsum__check_experiment_design_countfile |
| dimsum__check_files_exist | dimsum__check_files_exist |
| dimsum__check_variants | dimsum__check_variants |
| dimsum__concatenate_reads | dimsum__concatenate_reads |
| dimsum__convert_linked_adapters | dimsum__convert_linked_adapters |
| dimsum__create_dir | dimsum__create_dir |
| dimsum__cutadapt_report | dimsum__cutadapt_report |
| dimsum__debarcode_variants | dimsum__debarcode_variants |
| dimsum__demultiplex_cp_helper | dimsum__demultiplex_cp_helper |
| dimsum__demultiplex_helper | dimsum__demultiplex_helper |
| dimsum__derange_df | dimsum__derange_df |
| dimsum__detect_sequence_type | dimsum__detect_sequence_type |
| dimsum__diagnostics_report | dimsum__diagnostics_report |
| dimsum__error_model | dimsum__error_model |
| dimsum__error_model_qqplot | dimsum__error_model_qqplot |
| dimsum__fastqc_report | dimsum__fastqc_report |
| dimsum__filter_nuc_variants | dimsum__filter_nuc_variants |
| dimsum__filter_reads | dimsum__filter_reads |
| dimsum__filter_reads_helper | dimsum__filter_reads_helper |
| dimsum__filter_single_end_reads | dimsum__filter_single_end_reads |
| dimsum__filter_variants_coding | dimsum__filter_variants_coding |
| dimsum__filter_variants_noncoding | dimsum__filter_variants_noncoding |
| dimsum__fit_error_model | dimsum__fit_error_model |
| dimsum__fit_error_model_bootstrap | dimsum__fit_error_model_bootstrap |
| dimsum__get_barcode_design | dimsum__get_barcode_design |
| dimsum__get_cutadapt_options | dimsum__get_cutadapt_options |
| dimsum__get_experiment_design | dimsum__get_experiment_design |
| dimsum__get_synonymsequences | dimsum__get_synonymsequences |
| dimsum__gg_color_hue | dimsum__gg_color_hue |
| dimsum__ggpairs_binhex | dimsum__ggpairs_binhex |
| dimsum__hamming_distance | dimsum__hamming_distance |
| dimsum__identify_double_aa_mutations | dimsum__identify_double_aa_mutations |
| dimsum__identify_double_nt_mutations | dimsum__identify_double_nt_mutations |
| dimsum__identify_permitted_mutations | dimsum__identify_permitted_mutations |
| dimsum__identify_single_aa_mutations | dimsum__identify_single_aa_mutations |
| dimsum__identify_single_nt_mutations | dimsum__identify_single_nt_mutations |
| dimsum__identify_STOP_mutations | dimsum__identify_STOP_mutations |
| dimsum__infer_growth_rates | dimsum__infer_growth_rates |
| dimsum__merge_fitness | dimsum__merge_fitness |
| dimsum__merge_report | dimsum__merge_report |
| dimsum__normalise_fitness | dimsum__normalise_fitness |
| dimsum__parse_cutadapt_output | dimsum__parse_cutadapt_output |
| dimsum__parse_cutadapt_output_single_end | dimsum__parse_cutadapt_output_single_end |
| dimsum__parse_minimum_read_count_arguments | dimsum__parse_minimum_read_count_arguments |
| dimsum__plot_samplename | dimsum__plot_samplename |
| dimsum__process_merged_variants | dimsum__process_merged_variants |
| dimsum__range_df | dimsum__range_df |
| dimsum__remove_internal_constant_region | dimsum__remove_internal_constant_region |
| dimsum__render_report | dimsum__render_report |
| dimsum__replicate_fitness_deviation | dimsum__replicate_fitness_deviation |
| dimsum__sample_count_distributions | dimsum__sample_count_distributions |
| dimsum__save_metadata | dimsum__save_metadata |
| dimsum__save_png | dimsum__save_png |
| dimsum_stage_counts_to_fitness | dimsum_stage_counts_to_fitness |
| dimsum_stage_cutadapt | dimsum_stage_cutadapt |
| dimsum_stage_demultiplex | dimsum_stage_demultiplex |
| dimsum_stage_fastqc | dimsum_stage_fastqc |
| dimsum_stage_merge | dimsum_stage_merge |
| dimsum_stage_unique | dimsum_stage_unique |
| dimsum_stage_unzip | dimsum_stage_unzip |
| dimsum_stage_vsearch | dimsum_stage_vsearch |
| dimsum__status_message | dimsum__status_message |
| dimsum__sum_datatable_columns | dimsum__sum_datatable_columns |
| dimsum__swap_reads | dimsum__swap_reads |
| dimsum__unique_helper | dimsum__unique_helper |
| dimsum__unzip_helper | dimsum__unzip_helper |
| dimsum__validate_input | dimsum__validate_input |
| dimsum__vsearch_report | dimsum__vsearch_report |
| dimsum__vsearch_single_end_library_helper | dimsum__vsearch_single_end_library_helper |
| dimsum__vsearch_trans_library_helper | dimsum__vsearch_trans_library_helper |
| dimsum__writeFastq | dimsum__writeFastq |
