NAMESPACE

# Generated by roxygen2: do not edit by hand

export(MassExpressionTOProtCountV2)
export(SEToLongDT)
export(computeImputedCounts)
export(computeReplicateCounts)
export(createCompleteIntensityExperiment)
export(createSummarizedExperiment)
export(generate_qc_report)
export(generate_separate_qc_reports)
export(imputeLFQ)
export(initialiseLongIntensityDT)
export(limmaStatsFun)
export(listComparisonExperiments)
export(makeRLEBoxplotInteractive)
export(normaliseIntensity)
export(oneGroupReplDataV2)
export(oneProteinReplData)
export(plot_chosen_pca_experiment)
export(plot_condition_cv_distribution)
export(plot_consistent_proteins_by_replicate)
export(plot_density_distr)
export(plot_imputed_vs_not)
export(plot_log_measurement_boxplot)
export(plot_ma)
export(plot_mds_experiment)
export(plot_missingness_heatmap)
export(plot_n_identified_proteins_by_replicate)
export(plot_pca_experiment)
export(plot_protein_missingness)
export(plot_replicate_measured_values)
export(plot_rle_boxplot)
export(plot_samples_correlation_matrix)
export(plot_volcano)
export(prepareForFiltering)
export(preparePlottingData)
export(runGenericDiscovery)
export(runLimmaPipeline)
export(sanitize_strings)
export(sanitize_strings_in_dataframe)
export(saveOutput)
export(writeLimmaStatisticsTable)
export(writeOutputFile)
export(writeProteinQuantIntensities)
export(writeProteinViz)
export(writeReplicateData)
export(writeReplicateDataV2)
import(Biobase)
import(ComplexHeatmap)
import(FactoMineR)
import(SummarizedExperiment)
import(data.table)
import(dplyr)
import(factoextra)
import(foreach)
import(ggplot2)
import(limma)
import(parallel)
import(stringr)
import(tibble)
import(tidyr)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,metadata)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,dcast.data.table)
importFrom(data.table,rbindlist)
importFrom(data.table,setnames)
importFrom(dplyr,as_tibble)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,rename)
importFrom(dplyr,row_number)
importFrom(dplyr,summarize)
importFrom(jsonlite,unbox)
importFrom(jsonlite,write_json)
importFrom(stringr,str_c)
importFrom(stringr,str_detect)
importFrom(stringr,str_order)
importFrom(stringr,str_sort)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(uuid,UUIDgenerate)