Man pages for lehner-lab/DiMSum
A pipeline for processing deep mutational scanning data

dimsumRun DiMSum pipeline
dimsum__aggregate_AA_variantsdimsum__aggregate_AA_variants
dimsum__aggregate_AA_variants_fitnessdimsum__aggregate_AA_variants_fitness
dimsum__bayesian_double_fitnessdimsum__bayesian_double_fitness
dimsum__calculate_fitnessdimsum__calculate_fitness
dimsum__cbind_filldimsum__cbind_fill
dimsum__check_barcode_designdimsum__check_barcode_design
dimsum__check_countfiledimsum__check_countfile
dimsum__check_experiment_designdimsum__check_experiment_design
dimsum__check_experiment_design_countfiledimsum__check_experiment_design_countfile
dimsum__check_files_existdimsum__check_files_exist
dimsum__check_variantsdimsum__check_variants
dimsum__concatenate_readsdimsum__concatenate_reads
dimsum__convert_linked_adaptersdimsum__convert_linked_adapters
dimsum__create_dirdimsum__create_dir
dimsum__cutadapt_reportdimsum__cutadapt_report
dimsum__debarcode_variantsdimsum__debarcode_variants
dimsum__demultiplex_cp_helperdimsum__demultiplex_cp_helper
dimsum__demultiplex_helperdimsum__demultiplex_helper
dimsum__derange_dfdimsum__derange_df
dimsum__detect_sequence_typedimsum__detect_sequence_type
dimsum__diagnostics_reportdimsum__diagnostics_report
dimsum__error_modeldimsum__error_model
dimsum__error_model_qqplotdimsum__error_model_qqplot
dimsum__fastqc_reportdimsum__fastqc_report
dimsum__fastq_splitterdimsum__fastq_splitter
dimsum__filter_nuc_variantsdimsum__filter_nuc_variants
dimsum__filter_readsdimsum__filter_reads
dimsum__filter_reads_helperdimsum__filter_reads_helper
dimsum__filter_single_end_readsdimsum__filter_single_end_reads
dimsum__filter_variants_codingdimsum__filter_variants_coding
dimsum__filter_variants_noncodingdimsum__filter_variants_noncoding
dimsum__fit_error_modeldimsum__fit_error_model
dimsum__fit_error_model_bootstrapdimsum__fit_error_model_bootstrap
dimsum__get_barcode_designdimsum__get_barcode_design
dimsum__get_cutadapt_optionsdimsum__get_cutadapt_options
dimsum__get_experiment_designdimsum__get_experiment_design
dimsum__gg_color_huedimsum__gg_color_hue
dimsum__ggpairs_binhexdimsum__ggpairs_binhex
dimsum__hamming_distancedimsum__hamming_distance
dimsum__identify_double_aa_mutationsdimsum__identify_double_aa_mutations
dimsum__identify_double_nt_mutationsdimsum__identify_double_nt_mutations
dimsum__identify_permitted_mutationsdimsum__identify_permitted_mutations
dimsum__identify_single_aa_mutationsdimsum__identify_single_aa_mutations
dimsum__identify_single_nt_mutationsdimsum__identify_single_nt_mutations
dimsum__identify_STOP_mutationsdimsum__identify_STOP_mutations
dimsum__infer_growth_ratesdimsum__infer_growth_rates
dimsum__merge_fitnessdimsum__merge_fitness
dimsum__merge_reportdimsum__merge_report
dimsum__normalise_fitnessdimsum__normalise_fitness
dimsum__parse_cutadapt_outputdimsum__parse_cutadapt_output
dimsum__parse_cutadapt_output_single_enddimsum__parse_cutadapt_output_single_end
dimsum__parse_minimum_read_count_argumentsdimsum__parse_minimum_read_count_arguments
dimsum__plot_samplenamedimsum__plot_samplename
dimsum__process_merged_variantsdimsum__process_merged_variants
dimsum__range_dfdimsum__range_df
dimsum__remove_internal_constant_regiondimsum__remove_internal_constant_region
dimsum__render_reportdimsum__render_report
dimsum__replicate_fitness_deviationdimsum__replicate_fitness_deviation
dimsum__sample_count_distributionsdimsum__sample_count_distributions
dimsum__save_metadatadimsum__save_metadata
dimsum__save_pngdimsum__save_png
dimsum__split_helperdimsum__split_helper
dimsum_stage_counts_to_fitnessdimsum_stage_counts_to_fitness
dimsum_stage_cutadaptdimsum_stage_cutadapt
dimsum_stage_demultiplexdimsum_stage_demultiplex
dimsum_stage_fastqcdimsum_stage_fastqc
dimsum_stage_mergedimsum_stage_merge
dimsum_stage_splitdimsum_stage_split
dimsum_stage_uniquedimsum_stage_unique
dimsum_stage_unzipdimsum_stage_unzip
dimsum_stage_vsearchdimsum_stage_vsearch
dimsum__status_messagedimsum__status_message
dimsum__sum_datatable_columnsdimsum__sum_datatable_columns
dimsum__swap_readsdimsum__swap_reads
dimsum__unique_helperdimsum__unique_helper
dimsum__unzip_helperdimsum__unzip_helper
dimsum__validate_inputdimsum__validate_input
dimsum__vsearch_reportdimsum__vsearch_report
dimsum__vsearch_single_end_library_helperdimsum__vsearch_single_end_library_helper
dimsum__vsearch_trans_library_helperdimsum__vsearch_trans_library_helper
dimsum__writeFastqdimsum__writeFastq
lehner-lab/DiMSum documentation built on Sept. 15, 2021, 12:43 a.m.