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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(.summarise_missing_contrasts)
export(AnalysisConfiguration)
export(AnalysisParameters)
export(AnalysisTableAnnotation)
export(Benchmark)
export(Contrasts)
export(ContrastsInterface)
export(ContrastsMissing)
export(ContrastsModerated)
export(ContrastsPlotter)
export(ContrastsProDA)
export(ContrastsROPECA)
export(ContrastsTable)
export(LFQData)
export(LFQDataAggregator)
export(LFQDataPlotter)
export(LFQDataStats)
export(LFQDataSummariser)
export(LFQDataToSummarizedExperiment)
export(LFQDataTransformer)
export(LFQDataWriter)
export(LR_test)
export(MissingHelpers)
export(Model)
export(ModelInterface)
export(R6_extract_values)
export(UpSet_interaction_missing_stats)
export(UpSet_missing_stats)
export(adjust_p_values)
export(aggregate_intensity_topN)
export(apply_to_response_matrix)
export(build_model)
export(complete_cases)
export(compute_pooled)
export(contrasts_fisher_exact)
export(contrasts_linfct)
export(cor_jackknife_matrix)
export(cor_order)
export(create_config_MQ_peptide)
export(create_config_MSFragger_MSstats)
export(create_config_Skyline)
export(create_config_Spectronaut_Peptide)
export(estimate_intensity)
export(filter_byQValue)
export(filter_difference)
export(filter_proteins_by_peptide_count)
export(find_package_file)
export(get_UniprotID_from_fasta_header)
export(get_anova_df)
export(get_complete_model_fit)
export(get_contrast)
export(get_p_values_pbeta)
export(get_robscales)
export(hierarchy_counts)
export(hierarchy_counts_sample)
export(intensity_summary_by_hkeys)
export(interaction_missing_stats)
export(ionstar_bench_preprocess)
export(isSingular_lm)
export(jackknife)
export(jackknife_matrix)
export(lfq_power_t_test_proteins)
export(lfq_power_t_test_quantiles)
export(lfq_power_t_test_quantiles_V2)
export(lfq_write_table)
export(linfct_all_possible_contrasts)
export(linfct_factors_contrasts)
export(linfct_from_model)
export(linfct_matrix_contrasts)
export(make_benchmark)
export(make_interaction_column)
export(make_reduced_hierarchy_config)
export(matrix_to_tibble)
export(medpolish_estimate)
export(medpolish_estimate_df)
export(medpolish_estimate_dfconfig)
export(medpolish_protein_estimates)
export(merge_contrasts_results)
export(missigness_histogram)
export(missingness_per_condition)
export(missingness_per_condition_cumsum)
export(model_analyse)
export(model_summary)
export(moderated_p_limma)
export(moderated_p_limma_long)
export(ms_bench_add_scores)
export(ms_bench_auc)
export(multigroup_volcano)
export(my_contest)
export(my_contrast)
export(my_contrast_V1)
export(my_contrast_V2)
export(my_glht)
export(names_to_matrix)
export(normalize_log2_robscale)
export(nr_B_in_A)
export(nr_B_in_A_per_sample)
export(nr_obs_experiment)
export(nr_obs_sample)
export(old2new)
export(pairs_smooth)
export(pairs_w_abline)
export(panel_cor)
export(panel_hist)
export(pivot_model_contrasts_2_Wide)
export(plot_NA_heatmap)
export(plot_estimate)
export(plot_heatmap)
export(plot_heatmap_cor)
export(plot_heatmap_cor_iheatmap)
export(plot_hierarchies_add_quantline)
export(plot_hierarchies_boxplot)
export(plot_hierarchies_boxplot_df)
export(plot_hierarchies_line)
export(plot_hierarchies_line_df)
export(plot_intensity_distribution_density)
export(plot_intensity_distribution_violin)
export(plot_lmer_peptide_predictions)
export(plot_pca)
export(plot_raster)
export(plot_sample_correlation)
export(plot_screeplot)
export(plot_stat_density)
export(plot_stat_density_median)
export(plot_stat_violin)
export(plot_stat_violin_median)
export(plot_stdv_vs_mean)
export(poolvar)
export(prolfqua_data)
export(rank_by_NA)
export(rank_peptide_by_intensity)
export(remove_NA_rows)
export(remove_large_QValues)
export(remove_small_intensities)
export(render_MQSummary_rmd)
export(response_as_matrix)
export(response_matrix_as_tibble)
export(rlm_estimate)
export(rlm_estimate_dfconfig)
export(robust_scale)
export(sample_subset)
export(scale_with_subset)
export(scale_with_subset_by_factors)
export(scriptCopyHelperVec)
export(separate_factors)
export(separate_hierarchy)
export(setup_analysis)
export(sim_build_models_lm)
export(sim_build_models_lmer)
export(sim_lfq_data)
export(sim_lfq_data_2Factor_config)
export(sim_lfq_data_peptide_config)
export(sim_lfq_data_protein_config)
export(sim_make_model_lm)
export(sim_make_model_lmer)
export(spread_response_by_IsotopeLabel)
export(squeezeVarRob)
export(strategy_glm)
export(strategy_lm)
export(strategy_lmer)
export(strategy_rlm)
export(summarise_QValues)
export(summarize_hierarchy)
export(summarize_stats)
export(summarize_stats_all)
export(summarize_stats_factors)
export(summarize_stats_quantiles)
export(summary_ROPECA_median_p.scaled)
export(table_facade)
export(table_factors)
export(table_factors_size)
export(tidy_to_wide)
export(tidy_to_wide_config)
export(transform_work_intensity)
export(volcano_plotly)
export(which_missing)
import(dplyr)
import(ggplot2)
importFrom(MASS,rlm)
importFrom(conflicted,conflict_prefer)
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,anti_join)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,count)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,group_by_at)
importFrom(dplyr,inner_join)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,nest_by)
importFrom(dplyr,one_of)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,select_at)
importFrom(dplyr,starts_with)
importFrom(dplyr,summarize)
importFrom(dplyr,summarize_at)
importFrom(dplyr,ungroup)
importFrom(dplyr,vars)
importFrom(forcats,fct_relevel)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guides)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,stat_summary)
importFrom(ggplot2,theme)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(grDevices,rainbow)
importFrom(graphics,abline)
importFrom(graphics,hist)
importFrom(graphics,pairs)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,rect)
importFrom(graphics,text)
importFrom(gridExtra,grid.arrange)
importFrom(htmlwidgets,saveWidget)
importFrom(pheatmap,pheatmap)
importFrom(plotly,ggplotly)
importFrom(purrr,map)
importFrom(purrr,map2)
importFrom(purrr,map2_dbl)
importFrom(purrr,map_chr)
importFrom(purrr,map_dbl)
importFrom(purrr,map_df)
importFrom(purrr,map_dfc)
importFrom(purrr,map_if)
importFrom(purrr,map_int)
importFrom(purrr,map_lgl)
importFrom(purrr,reduce)
importFrom(rlang,":=")
importFrom(rlang,.data)
importFrom(rlang,UQ)
importFrom(rlang,sym)
importFrom(rlang,syms)
importFrom(stats,.lm.fit)
importFrom(stats,anova)
importFrom(stats,as.formula)
importFrom(stats,coef)
importFrom(stats,coefficients)
importFrom(stats,confint)
importFrom(stats,cor)
importFrom(stats,cor.test)
importFrom(stats,df.residual)
importFrom(stats,ecdf)
importFrom(stats,formula)
importFrom(stats,glm)
importFrom(stats,lm)
importFrom(stats,mad)
importFrom(stats,median)
importFrom(stats,medpolish)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,pbeta)
importFrom(stats,power.t.test)
importFrom(stats,prcomp)
importFrom(stats,predict)
importFrom(stats,pt)
importFrom(stats,qt)
importFrom(stats,quantile)
importFrom(stats,residuals)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,sigma)
importFrom(stats,terms)
importFrom(stats,update)
importFrom(stats,vcov)
importFrom(stringr,str_trim)
importFrom(tibble,add_column)
importFrom(tibble,as_tibble)
importFrom(tibble,column_to_rownames)
importFrom(tibble,tibble)
importFrom(tidyr,gather)
importFrom(tidyr,nest)
importFrom(tidyr,nesting)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,separate)
importFrom(tidyr,separate_rows)
importFrom(tidyr,spread)
importFrom(tidyr,unite)
importFrom(tidyr,unnest)
importFrom(tidyr,unnest_legacy)
importFrom(utils,combn)
importFrom(utils,data)
importFrom(utils,head)
importFrom(utils,read.csv)
importFrom(utils,tail)
importFrom(utils,unzip)
importFrom(yaml,write_yaml)