| add_contrast |
Man page
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| add_protein_prettyprint_label |
Man page
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| adjust_modes |
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| aggregate_tibble_by_datatables |
Man page
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| analysis_quickstart |
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| append_log |
Man page
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| append_log_error |
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| append_log_timestamp |
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| as_matrix_except_first_column |
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| assert_lme4_functional |
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| boxplot_add_text |
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| cache_filtering_data |
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| check_dataset_hascache |
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| check_dataset_integrity |
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| check_parameter_is_boolean |
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| check_parameter_is_numeric |
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| check_parameter_is_string |
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| check_valid_tibble_peptides |
Man page
Source code
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| check_valid_tibble_proteins |
Man page
Source code
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| check_valid_tibble_samples |
Man page
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| coefficient_of_variation |
Man page
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| coefficient_of_variation_vectorized |
Man page
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| column_intensity_to_label |
Man page
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| contrast_to_samplegroups |
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| count_sep_char |
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| dataset_filter_custom |
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| dataset_transfer_peptide_properties |
Man page
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| de_deqms |
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| de_ebayes |
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| de_msempire |
Man page
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| de_msqrob_customformula |
Man page
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| de_msqrobsum_msqrob |
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| dea |
Man page
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| dea_algorithms |
Man page
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| dea_algorithms_reserved |
Man page
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| dea_protein_background_foldchange_limits |
Man page
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| dea_results_to_wide |
Man page
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| dea_summary_prettyprint |
Man page
Source code
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| diffdetect_results_to_wide |
Man page
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| diffdetect_summary_prettyprint |
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| differential_detect |
Man page
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| differential_detection_filter |
Man page
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| disambiguate_protein_table_by_gene |
Man page
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| empty_protein_tibble |
Man page
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| enforce_sample_value_types |
Man page
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| error_legacy_contrast_definitions |
Man page
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| export_peptide_abundance_matrix |
Man page
Source code
|
| export_protein_abundance_matrix |
Man page
Source code
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| export_statistical_results |
Man page
Source code
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| export_stats_genesummary |
Man page
Source code
|
| fasta_header_to_gene |
Man page
Source code
|
| fasta_header_to_id |
Man page
Source code
|
| fasta_id_short |
Man page
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| fasta_identifier_isdecoy |
Man page
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| fasta_parse_file |
Man page
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| file_check |
Man page
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| filename_extract_extension |
Man page
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| filename_strip_illegal_characters |
Man page
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| filter_dataset |
Man page
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| fit_t_dist_fixed_mu |
Man page
Source code
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| format_r_code |
Man page
Source code
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| fragpipe_find_psm_files |
Man page
Source code
|
| fragpipe_map_combined_protein |
Man page
Source code
|
| fragpipe_modification_to_instruction__legacy |
Man page
|
| fragpipe_modseq_compose |
Man page
Source code
|
| fragpipe_parse_msstats |
Man page
Source code
|
| fragpipe_parse_psm |
Man page
Source code
|
| fragpipe_parse_quant |
Man page
Source code
|
| fragpipe_peptideresults_to_dataset |
Man page
Source code
|
| generate_pdf_report |
Man page
Source code
|
| get_column_intensity |
Man page
Source code
|
| get_mode |
Man page
Source code
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| get_peptide_filternorm_variants |
Man page
Source code
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| get_protein_matrix |
Man page
Source code
|
| get_samples_for_regression |
Man page
Source code
|
| gg_color_hue |
Man page
Source code
|
| ggplot_coefficient_of_variation |
Man page
|
| ggplot_coefficient_of_variation__leave_one_out |
Man page
|
| ggplot_peptide_abundances |
Man page
Source code
|
| ggplot_peptide_detect_frequency |
Man page
Source code
|
| ggplot_peptide_detect_frequency_distribution |
Man page
Source code
|
| ggplot_sample_detect_counts_barplots |
Man page
Source code
|
| ggplot_sample_detect_vs_metadata_scatterplot |
Man page
Source code
|
| ggplot_sample_detect_vs_metadata_scatterplot_by_prop |
Man page
Source code
|
| ggplot_split_legend |
Man page
Source code
|
| has_legacy_contrast_definitions |
Man page
Source code
|
| hgnc_add_xrefs |
Man page
Source code
|
| hgnc_lookuptable |
Man page
Source code
|
| idmap_symbols |
Man page
Source code
|
| idmap_uniprotid |
Man page
Source code
|
| import_dataset_diann |
Man page
Source code
|
| import_dataset_encyclopedia |
Man page
Source code
|
| import_dataset_fragpipe_ionquant |
Man page
Source code
|
| import_dataset_fragpipe_ionquant__legacy |
Man page
Source code
|
| import_dataset_fragpipe_psm_file |
Man page
Source code
|
| import_dataset_in_long_format |
Man page
Source code
|
| import_dataset_maxquant_evidencetxt |
Man page
Source code
|
| import_dataset_metamorpheus |
Man page
Source code
|
| import_dataset_openms_mztab |
Man page
Source code
|
| import_dataset_openswath |
Man page
Source code
|
| import_dataset_peaks |
Man page
Source code
|
| import_dataset_proteomediscoverer_txt |
Man page
Source code
|
| import_dataset_skyline |
Man page
Source code
|
| import_dataset_spectronaut |
Man page
Source code
|
| import_expressionset |
Man page
Source code
|
| import_fasta |
Man page
Source code
|
| import_maxquant_peptides |
Man page
Source code
|
| import_maxquant_proteingroups |
Man page
Source code
|
| import_metamorpheus_proteingroups |
Man page
Source code
|
| import_metamorpheus_quantifiedpeaks |
Man page
Source code
|
| import_protein_metadata_from_fasta |
Man page
|
| import_sample_metadata |
Man page
Source code
|
| initialize_multiprocessing |
Man page
Source code
|
| invalidate_cache |
Man page
Source code
|
| is_dia_dataset |
Man page
Source code
|
| limma_fit_extract_stats |
Man page
Source code
|
| limma_wrapper |
Man page
Source code
|
| log2_to_ln |
Man page
Source code
|
| log_peptide_tibble_pep_prot_counts |
Man page
Source code
|
| log_type_to_color |
Source code
|
| logger.default |
Man page
Source code
|
| make_bins |
Man page
Source code
|
| map_headers |
Man page
Source code
|
| matrix_grouped_column_aggregate |
Man page
Source code
|
| matrix_to_long |
Man page
Source code
|
| merge_fractionated_samples |
Man page
|
| merge_proteingroups_by_gene |
Man page
|
| merge_replicate_samples |
Man page
Source code
|
| metadata_matrix_from_filenames |
Man page
Source code
|
| mgi_lookuptable |
Man page
Source code
|
| minlog10 |
Man page
Source code
|
| msdap |
Man page
|
| msdap-package |
Man page
|
| msdap_version |
Man page
Source code
|
| msqrobsum |
Source code
|
| norm_scales_fcmode |
Man page
Source code
|
| norm_scales_var |
Man page
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|
| normalization_algorithms |
Man page
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|
| normalize_matrix |
Man page
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|
| normalize_median |
Man page
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|
| normalize_modebetween_protein |
Man page
Source code
|
| normalize_msempire |
Man page
Source code
|
| normalize_peptide_intensity_column |
Man page
|
| normalize_rlr |
Man page
Source code
|
| normalize_rlr_MSqRob_implementation |
Man page
Source code
|
| normalize_vwmb |
Man page
Source code
|
| pairwise_modes |
Man page
Source code
|
| parse_fragpipe_proteins__legacy |
Man page
|
| parse_fragpipe_proteins_from_combined_proteins |
Man page
Source code
|
| path_append_and_check |
Man page
Source code
|
| path_clean_slashes |
Man page
Source code
|
| path_exists |
Man page
Source code
|
| pdf_combine_chunks |
Man page
Source code
|
| peptide_and_protein_counts_per_sample |
Man page
Source code
|
| peptides_collapse_by_sequence |
Man page
Source code
|
| permute_ab |
Man page
Source code
|
| plot_abundance_distributions |
Man page
Source code
|
| plot_benchmark_volcano |
Man page
Source code
|
| plot_dia_cscore_histograms |
Man page
Source code
|
| plot_differential_detect |
Man page
Source code
|
| plot_foldchange_distribution_among_replicates |
Man page
Source code
|
| plot_foldchanges |
Man page
Source code
|
| plot_peptide_data |
Man page
Source code
|
| plot_peptide_data_by_contrast_to_pdf |
Man page
Source code
|
| plot_pvalue_histogram |
Man page
Source code
|
| plot_retention_time_v2 |
Man page
Source code
|
| plot_roc |
Man page
Source code
|
| plot_sample_pca |
Man page
Source code
|
| plot_sample_pca__sample_in_contrast |
Man page
Source code
|
| plot_true_false_positive_counts |
Man page
Source code
|
| plot_variance_explained |
Man page
Source code
|
| plot_volcano |
Man page
Source code
|
| plot_volcano_allcontrast |
Man page
Source code
|
| print_available_filtering_results |
Man page
Source code
|
| print_contrasts |
Man page
Source code
|
| print_dataset_summary |
Man page
Source code
|
| protein_eset_from_data |
Man page
Source code
|
| proteingroup_to_idshort_lookuptable |
Man page
Source code
|
| read_table_by_header_spec |
Man page
Source code
|
| read_textfile_compressed |
Man page
Source code
|
| reduce_ggplot_object_size |
Man page
Source code
|
| reformat_date |
Man page
Source code
|
| regex_classification |
Man page
Source code
|
| regex_rawfile_strip_extension |
Man page
Source code
|
| reintroduce_filtered_intensities |
Source code
|
| remove_by_charlength |
Man page
Source code
|
| remove_contrasts |
Man page
Source code
|
| remove_file_extension_from_path |
Man page
Source code
|
| remove_file_if_exists |
Man page
Source code
|
| remove_proteins_by_name |
Man page
Source code
|
| replace_inf_with_NA |
Man page
Source code
|
| replace_nonfinite |
Man page
Source code
|
| replace_zero_with_NA |
Man page
Source code
|
| reset_log |
Man page
Source code
|
| rgd_lookuptable |
Man page
Source code
|
| rmarkdown_xtable_custom |
Man page
Source code
|
| robust_header_matching |
Man page
Source code
|
| rollup_pep2prot |
Man page
Source code
|
| rollup_pep2prot_maxlfq |
Man page
Source code
|
| rollup_pep2prot_summation |
Man page
Source code
|
| rollup_pep2prot_tmp |
Man page
Source code
|
| sample_color_coding |
Man page
Source code
|
| sample_color_coding__long_format |
Man page
Source code
|
| sample_metadata_custom |
Man page
Source code
|
| sample_metadata_from_file |
Man page
Source code
|
| sample_metadata_from_filenames |
Man page
Source code
|
| sample_metadata_sort_and_filter |
Man page
Source code
|
| scale_between_quantiles |
Man page
Source code
|
| score_classification_counts |
Man page
Source code
|
| setup_contrasts |
Man page
Source code
|
| shift_empty |
Man page
Source code
|
| smooth_loess_custom |
Man page
Source code
|
| split_alt_sep_char |
Man page
Source code
|
| split_array |
Man page
Source code
|
| split_char_num |
Man page
Source code
|
| split_generic |
Man page
Source code
|
| split_recursively |
Man page
Source code
|
| strip_common_substring |
Man page
Source code
|
| subchunkify |
Man page
Source code
|
| subset_protein_eset_for_dea |
Man page
Source code
|
| subset_relevant_code_snippet_for_report |
Man page
Source code
|
| summarise_stats |
Man page
Source code
|
| summarise_stats__for_contrast |
Man page
Source code
|
| threshold_numerics |
Man page
Source code
|
| tibble_as_eset |
Man page
Source code
|
| tibble_peptides_reorder |
Man page
Source code
|
| update_protein_mapping |
Man page
Source code
|
| update_protein_mapping_from_maxquant |
Man page
Source code
|
| user_provided_metadata |
Man page
Source code
|
| validate_eset_fitdata |
Man page
Source code
|
| write_template_for_sample_metadata |
Man page
Source code
|
