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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(EINPROT_COMPLEXES_FILE)
export(EINPROT_POMBASE_CONVTABLE)
export(EINPROT_WORMBASE_CONVTABLE)
export(addSampleAnnots)
export(combineIds)
export(defineAssayNames)
export(doImputation)
export(doNormalization)
export(doPCA)
export(emptySampleText)
export(expDesignText)
export(filterByModText)
export(filterFragPipe)
export(filterMaxQuant)
export(filterPDTMT)
export(filterSpectronaut)
export(fixFeatureIds)
export(formatTableColumns)
export(getCalibrationFrompdAnalysis)
export(getColumnNames)
export(getContaminantsDatabaseFrompdAnalysis)
export(getConvTable)
export(getFirstId)
export(getIntensityColumns)
export(getMatSubtractedBaseline)
export(getMaxMissedCleavagesFrompdAnalysis)
export(getNthId)
export(getPSMValidationInfoFrompdAnalysis)
export(getQuantInfoFrompdAnalysis)
export(getQuantOrderFrompdAnalysis)
export(getSearchParametersFrompdAnalysis)
export(getSpeciesInfo)
export(getSupportedSpecies)
export(getTemplateNamesFrompdAnalysis)
export(getUniProtToIDMapping)
export(getValidationInfoFrompdAnalysis)
export(importDIANN)
export(importExperiment)
export(importSpectronaut)
export(inputText)
export(introText)
export(listComplexDBs)
export(makeAbundanceExport)
export(makeAbundanceHeatmap)
export(makeComplexDB)
export(makeDbLinkTable)
export(makeIntensityBoxplots)
export(makeListOfComparisons)
export(makeMeanSDPlot)
export(makeSAPlot)
export(makeTableFromList)
export(makeiSEEScript)
export(normText)
export(plotDetectedInSamples)
export(plotFractionDetectedPerSample)
export(plotImputationDistribution)
export(plotMissingValuesHeatmap)
export(plotVolcano)
export(prepareFeatureCollections)
export(prepareFinalSCE)
export(readDIANNInfo)
export(readFragPipeInfo)
export(readMaxQuantXML)
export(readProteomeDiscovererInfo)
export(readSpectronautSetup)
export(runDIANNAnalysis)
export(runFragPipeAnalysis)
export(runMaxQuantAnalysis)
export(runPDTMTAnalysis)
export(runPDTMTptmAnalysis)
export(runPTMTest)
export(runSpectronautAnalysis)
export(runTest)
export(saText)
export(seqLogoApp)
export(testText)
import(STRINGdb)
importFrom(BiocSingular,ExactParam)
importFrom(Biostrings,AAStringSet)
importFrom(Biostrings,consensusMatrix)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,columnAnnotation)
importFrom(ComplexHeatmap,draw)
importFrom(ComplexUpset,upset)
importFrom(DT,DTOutput)
importFrom(DT,datatable)
importFrom(DT,renderDT)
importFrom(ExploreModelMatrix,VisualizeDesign)
importFrom(GGally,ggpairs)
importFrom(IRanges,CharacterList)
importFrom(MsCoreUtils,impute_matrix)
importFrom(MsCoreUtils,normalizeMethods)
importFrom(QFeatures,readSummarizedExperiment)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,combineCols)
importFrom(S4Vectors,endoapply)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(XML,xmlParse)
importFrom(XML,xmlToList)
importFrom(babelgene,orthologs)
importFrom(circlize,colorRamp2)
importFrom(cowplot,plot_grid)
importFrom(cowplot,theme_cowplot)
importFrom(dplyr,"%>%")
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,arrange)
importFrom(dplyr,between)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,contains)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(dplyr,if_any)
importFrom(dplyr,last_col)
importFrom(dplyr,left_join)
importFrom(dplyr,matches)
importFrom(dplyr,mutate)
importFrom(dplyr,pull)
importFrom(dplyr,relocate)
importFrom(dplyr,rename)
importFrom(dplyr,row_number)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(dplyr,starts_with)
importFrom(dplyr,summarize)
importFrom(dplyr,tally)
importFrom(dplyr,ungroup)
importFrom(forcats,fct_reorder)
importFrom(genefilter,rowSds)
importFrom(genefilter,rowttests)
importFrom(ggalt,geom_encircle)
importFrom(ggiraph,geom_point_interactive)
importFrom(ggiraph,girafe_options)
importFrom(ggiraph,opts_hover)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expand_limits)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_errorbar)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_jitter)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,labs)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,position_jitterdodge)
importFrom(ggplot2,rel)
importFrom(ggplot2,scale_fill_gradient2)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_minimal)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,dev.off)
importFrom(grDevices,hcl)
importFrom(grDevices,pdf)
importFrom(grid,gpar)
importFrom(htmltools,tagList)
importFrom(iSEEu,registerAveAbFields)
importFrom(iSEEu,registerFeatureSetCollections)
importFrom(iSEEu,registerLogFCFields)
importFrom(iSEEu,registerPValueFields)
importFrom(imputeLCMD,impute.MinProb)
importFrom(kableExtra,column_spec)
importFrom(kableExtra,kable_paper)
importFrom(kableExtra,kbl)
importFrom(knitr,current_input)
importFrom(limma,cameraPR)
importFrom(limma,contrasts.fit)
importFrom(limma,eBayes)
importFrom(limma,ids2indices)
importFrom(limma,lmFit)
importFrom(limma,removeBatchEffect)
importFrom(limma,topTable)
importFrom(limma,topTreat)
importFrom(limma,treat)
importFrom(mclust,adjustedRandIndex)
importFrom(methods,as)
importFrom(methods,is)
importFrom(motifStack,colorset)
importFrom(motifStack,pcm2pfm)
importFrom(msigdbr,msigdbr)
importFrom(plotly,ggplotly)
importFrom(proDA,proDA)
importFrom(proDA,test_diff)
importFrom(readr,read_file)
importFrom(readr,read_tsv)
importFrom(readr,write_file)
importFrom(rlang,.data)
importFrom(rmarkdown,pandoc_available)
importFrom(rmarkdown,pandoc_exec)
importFrom(rmarkdown,render)
importFrom(rrcovNA,impSeqRob)
importFrom(scales,muted)
importFrom(scales,percent_format)
importFrom(scater,runPCA)
importFrom(scuttle,makePerCellDF)
importFrom(shiny,downloadButton)
importFrom(shiny,downloadHandler)
importFrom(shiny,fluidPage)
importFrom(shiny,mainPanel)
importFrom(shiny,plotOutput)
importFrom(shiny,reactive)
importFrom(shiny,renderPlot)
importFrom(shiny,renderText)
importFrom(shiny,shinyApp)
importFrom(shiny,sidebarLayout)
importFrom(shiny,sidebarPanel)
importFrom(shiny,textOutput)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,p.adjust)
importFrom(stats,pt)
importFrom(stats,quantile)
importFrom(stats,rnorm)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stringdist,amatch)
importFrom(stringr,str_extract)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,gather)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,separate)
importFrom(tidyr,separate_rows)
importFrom(tidyr,separate_wider_delim)
importFrom(tidyr,unite)
importFrom(tidyr,unnest)
importFrom(tidyselect,any_of)
importFrom(tools,file_ext)
importFrom(utils,combn)
importFrom(utils,download.file)
importFrom(utils,head)
importFrom(utils,packageVersion)
importFrom(utils,read.csv)
importFrom(utils,read.delim)
importFrom(utils,stack)
importFrom(utils,tail)
importFrom(utils,unzip)
importFrom(utils,write.table)
importFrom(utils,zip)
importFrom(writexl,write_xlsx)
importFrom(xfun,Rscript_call)
importFrom(xml2,read_xml)
importFrom(xml2,xml_attr)
importFrom(xml2,xml_find_all)
importFrom(xml2,xml_text)