Files in lehner-lab/DiMSum
A pipeline for processing deep mutational scanning data
DESCRIPTION
DMS_experiment.png
DiMSum
DiMSum.R
Dumpling.png
LICENSE
NAMESPACE
R/dimsum.R
R/dimsum__aggregate_AA_variants.R
R/dimsum__aggregate_AA_variants_fitness.R
R/dimsum__bayesian_double_fitness.R
R/dimsum__calculate_fitness.R
R/dimsum__cbind_fill.R
R/dimsum__check_barcode_design.R
R/dimsum__check_barcodeidentityfile.R
R/dimsum__check_countfile.R
R/dimsum__check_experiment_design.R
R/dimsum__check_experiment_design_countfile.R
R/dimsum__check_files_exist.R
R/dimsum__check_variants.R
R/dimsum__concatenate_reads.R
R/dimsum__convert_linked_adapters.R
R/dimsum__create_dir.R
R/dimsum__cutadapt_report.R
R/dimsum__debarcode_variants.R
R/dimsum__demultiplex_cp_helper.R
R/dimsum__demultiplex_helper.R
R/dimsum__derange_df.R
R/dimsum__detect_sequence_type.R
R/dimsum__diagnostics_report.R
R/dimsum__error_model.R
R/dimsum__error_model_qqplot.R
R/dimsum__fastqc_report.R
R/dimsum__filter_nuc_variants.R
R/dimsum__filter_reads.R
R/dimsum__filter_reads_helper.R
R/dimsum__filter_single_end_reads.R
R/dimsum__filter_variants_coding.R
R/dimsum__filter_variants_noncoding.R
R/dimsum__fit_error_model.R
R/dimsum__fit_error_model_bootstrap.R
R/dimsum__get_barcode_design.R
R/dimsum__get_cutadapt_options.R
R/dimsum__get_experiment_design.R
R/dimsum__get_synonymsequences.R
R/dimsum__gg_color_hue.R
R/dimsum__ggpairs_binhex.R
R/dimsum__hamming_distance.R
R/dimsum__identify_STOP_mutations.R
R/dimsum__identify_double_aa_mutations.R
R/dimsum__identify_double_nt_mutations.R
R/dimsum__identify_permitted_mutations.R
R/dimsum__identify_single_aa_mutations.R
R/dimsum__identify_single_nt_mutations.R
R/dimsum__infer_growth_rates.R
R/dimsum__merge_fitness.R
R/dimsum__merge_report.R
R/dimsum__normalise_fitness.R
R/dimsum__parse_cutadapt_output.R
R/dimsum__parse_cutadapt_output_single_end.R
R/dimsum__parse_minimum_read_count_arguments.R
R/dimsum__plot_samplename.R
R/dimsum__process_merged_variants.R
R/dimsum__range_df.R
R/dimsum__remove_internal_constant_region.R
R/dimsum__render_report.R
R/dimsum__replicate_fitness_deviation.R
R/dimsum__sample_count_distributions.R
R/dimsum__save_metadata.R
R/dimsum__save_png.R
R/dimsum__status_message.R
R/dimsum__sum_datatable_columns.R
R/dimsum__swap_reads.R
R/dimsum__unique_helper.R
R/dimsum__unzip_helper.R
R/dimsum__validate_input.R
R/dimsum__vsearch_report.R
R/dimsum__vsearch_single_end_library_helper.R
R/dimsum__vsearch_trans_library_helper.R
R/dimsum__writeFastq.R
R/dimsum_stage_counts_to_fitness.R
R/dimsum_stage_cutadapt.R
R/dimsum_stage_demultiplex.R
R/dimsum_stage_fastqc.R
R/dimsum_stage_merge.R
R/dimsum_stage_unique.R
R/dimsum_stage_unzip.R
R/dimsum_stage_vsearch.R
README.md
dimsum.yaml
docs/ARGUMENTS.md
docs/DEMO.md
docs/FILEFORMATS.md
docs/INSTALLATION.md
docs/PIPELINE.md
examples/example_barcodeDesign.txt
examples/example_experimentDesign.txt
examples/example_experimentDesign_gr.txt
examples/example_synonymSequences.txt
examples/example_variantCounts.txt
examples/example_variantIdentity.txt
inst/demo/countFile_Toy.txt
inst/demo/experimentDesign_Toy.txt
inst/rmd/Dumpling.png
inst/rmd/report.Rmd
man/dimsum.Rd
man/dimsum__aggregate_AA_variants.Rd
man/dimsum__aggregate_AA_variants_fitness.Rd
man/dimsum__bayesian_double_fitness.Rd
man/dimsum__calculate_fitness.Rd
man/dimsum__cbind_fill.Rd
man/dimsum__check_barcode_design.Rd
man/dimsum__check_barcodeidentityfile.Rd
man/dimsum__check_countfile.Rd
man/dimsum__check_experiment_design.Rd
man/dimsum__check_experiment_design_countfile.Rd
man/dimsum__check_files_exist.Rd
man/dimsum__check_variants.Rd
man/dimsum__concatenate_reads.Rd
man/dimsum__convert_linked_adapters.Rd
man/dimsum__create_dir.Rd
man/dimsum__cutadapt_report.Rd
man/dimsum__debarcode_variants.Rd
man/dimsum__demultiplex_cp_helper.Rd
man/dimsum__demultiplex_helper.Rd
man/dimsum__derange_df.Rd
man/dimsum__detect_sequence_type.Rd
man/dimsum__diagnostics_report.Rd
man/dimsum__error_model.Rd
man/dimsum__error_model_qqplot.Rd
man/dimsum__fastqc_report.Rd
man/dimsum__filter_nuc_variants.Rd
man/dimsum__filter_reads.Rd
man/dimsum__filter_reads_helper.Rd
man/dimsum__filter_single_end_reads.Rd
man/dimsum__filter_variants_coding.Rd
man/dimsum__filter_variants_noncoding.Rd
man/dimsum__fit_error_model.Rd
man/dimsum__fit_error_model_bootstrap.Rd
man/dimsum__get_barcode_design.Rd
man/dimsum__get_cutadapt_options.Rd
man/dimsum__get_experiment_design.Rd
man/dimsum__get_synonymsequences.Rd
man/dimsum__gg_color_hue.Rd
man/dimsum__ggpairs_binhex.Rd
man/dimsum__hamming_distance.Rd
man/dimsum__identify_STOP_mutations.Rd
man/dimsum__identify_double_aa_mutations.Rd
man/dimsum__identify_double_nt_mutations.Rd
man/dimsum__identify_permitted_mutations.Rd
man/dimsum__identify_single_aa_mutations.Rd
man/dimsum__identify_single_nt_mutations.Rd
man/dimsum__infer_growth_rates.Rd
man/dimsum__merge_fitness.Rd
man/dimsum__merge_report.Rd
man/dimsum__normalise_fitness.Rd
man/dimsum__parse_cutadapt_output.Rd
man/dimsum__parse_cutadapt_output_single_end.Rd
man/dimsum__parse_minimum_read_count_arguments.Rd
man/dimsum__plot_samplename.Rd
man/dimsum__process_merged_variants.Rd
man/dimsum__range_df.Rd
man/dimsum__remove_internal_constant_region.Rd
man/dimsum__render_report.Rd
man/dimsum__replicate_fitness_deviation.Rd
man/dimsum__sample_count_distributions.Rd
man/dimsum__save_metadata.Rd
man/dimsum__save_png.Rd
man/dimsum__status_message.Rd
man/dimsum__sum_datatable_columns.Rd
man/dimsum__swap_reads.Rd
man/dimsum__unique_helper.Rd
man/dimsum__unzip_helper.Rd
man/dimsum__validate_input.Rd
man/dimsum__vsearch_report.Rd
man/dimsum__vsearch_single_end_library_helper.Rd
man/dimsum__vsearch_trans_library_helper.Rd
man/dimsum__writeFastq.Rd
man/dimsum_stage_counts_to_fitness.Rd
man/dimsum_stage_cutadapt.Rd
man/dimsum_stage_demultiplex.Rd
man/dimsum_stage_fastqc.Rd
man/dimsum_stage_merge.Rd
man/dimsum_stage_unique.Rd
man/dimsum_stage_unzip.Rd
man/dimsum_stage_vsearch.Rd
