# A pipeline for processing deep mutational scanning data

## Documentation for package ‘DiMSum’ version 1.3

- DESCRIPTION file.
- Code demos. Use demo() to run them.

## Help Pages

dimsum | Run DiMSum pipeline
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__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_barcodeidentityfile | dimsum__check_barcodeidentityfile
dimsum__check_barcode_design | dimsum__check_barcode_design
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__ggpairs_binhex | dimsum__ggpairs_binhex
dimsum__gg_color_hue | dimsum__gg_color_hue
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__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