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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(add_contrast)
export(analysis_quickstart)
export(append_log)
export(as_matrix_except_first_column)
export(assert_lme4_functional)
export(cache_filtering_data)
export(check_dataset_hascache)
export(check_dataset_integrity)
export(check_valid_tibble_peptides)
export(check_valid_tibble_proteins)
export(check_valid_tibble_samples)
export(de_deqms)
export(de_ebayes)
export(de_msempire)
export(de_msqrobsum_msqrob)
export(dea)
export(dea_algorithms)
export(dea_algorithms_reserved)
export(dea_protein_background_foldchange_limits)
export(differential_detect)
export(differential_detection_filter)
export(export_peptide_abundance_matrix)
export(export_protein_abundance_matrix)
export(export_statistical_results)
export(export_stats_genesummary)
export(file_check)
export(filename_strip_illegal_characters)
export(filter_dataset)
export(generate_pdf_report)
export(get_peptide_filternorm_variants)
export(get_protein_matrix)
export(get_samples_for_regression)
export(has_legacy_contrast_definitions)
export(hgnc_lookuptable)
export(import_dataset_diann)
export(import_dataset_encyclopedia)
export(import_dataset_fragpipe_ionquant)
export(import_dataset_fragpipe_ionquant__legacy)
export(import_dataset_fragpipe_psm_file)
export(import_dataset_in_long_format)
export(import_dataset_maxquant_evidencetxt)
export(import_dataset_metamorpheus)
export(import_dataset_openms_mztab)
export(import_dataset_openswath)
export(import_dataset_peaks)
export(import_dataset_proteomediscoverer_txt)
export(import_dataset_skyline)
export(import_dataset_spectronaut)
export(import_expressionset)
export(import_fasta)
export(import_maxquant_peptides)
export(import_maxquant_proteingroups)
export(import_sample_metadata)
export(initialize_multiprocessing)
export(invalidate_cache)
export(is_dia_dataset)
export(limma_wrapper)
export(logger.default)
export(matrix_to_long)
export(merge_fractionated_samples)
export(merge_proteingroups_by_gene)
export(merge_replicate_samples)
export(mgi_lookuptable)
export(minlog10)
export(msdap_version)
export(normalization_algorithms)
export(normalize_matrix)
export(normalize_modebetween_protein)
export(normalize_peptide_intensity_column)
export(normalize_vwmb)
export(path_append_and_check)
export(path_exists)
export(plot_differential_detect)
export(plot_peptide_data)
export(plot_sample_pca__sample_in_contrast)
export(plot_variance_explained)
export(plot_volcano)
export(plot_volcano_allcontrast)
export(print_available_filtering_results)
export(print_contrasts)
export(print_dataset_summary)
export(protein_eset_from_data)
export(read_textfile_compressed)
export(regex_classification)
export(remove_contrasts)
export(remove_proteins_by_name)
export(reset_log)
export(rgd_lookuptable)
export(rollup_pep2prot)
export(rollup_pep2prot_maxlfq)
export(rollup_pep2prot_summation)
export(rollup_pep2prot_tmp)
export(sample_color_coding__long_format)
export(sample_metadata_custom)
export(setup_contrasts)
export(tibble_as_eset)
export(update_protein_mapping)
export(update_protein_mapping_from_maxquant)
export(user_provided_metadata)
export(write_template_for_sample_metadata)
import(dplyr)
import(ggplot2)
import(knitr)
import(tibble)
import(tidyr)
importFrom(Biobase,ExpressionSet)
importFrom(Biobase,annotatedDataFrameFrom)
importFrom(Biobase,classVersion)
importFrom(Biobase,exprs)
importFrom(Biobase,fData)
importFrom(Biobase,featureNames)
importFrom(Biobase,pData)
importFrom(BiocParallel,SerialParam)
importFrom(DBI,dbConnect)
importFrom(DBI,dbDisconnect)
importFrom(DBI,dbExistsTable)
importFrom(DBI,dbGetQuery)
importFrom(DBI,dbIsValid)
importFrom(DBI,dbListTables)
importFrom(MASS,psi.huber)
importFrom(MASS,rlm)
importFrom(RSQLite,SQLite)
importFrom(archive,archive_read)
importFrom(archive,file_read)
importFrom(colorspace,hcl_palettes)
importFrom(colorspace,sequential_hcl)
importFrom(crayon,blue)
importFrom(crayon,cyan)
importFrom(crayon,red)
importFrom(crayon,silver)
importFrom(data.table,"%chin%")
importFrom(data.table,as.data.table)
importFrom(data.table,chmatch)
importFrom(data.table,data.table)
importFrom(data.table,dcast)
importFrom(data.table,fread)
importFrom(data.table,fwrite)
importFrom(data.table,is.data.table)
importFrom(data.table,melt.data.table)
importFrom(data.table,merge.data.table)
importFrom(data.table,setDT)
importFrom(data.table,setkey)
importFrom(data.table,setorder)
importFrom(data.table,uniqueN)
importFrom(devtools,session_info)
importFrom(diann,diann_maxlfq)
importFrom(doParallel,registerDoParallel)
importFrom(foreach,"%dopar%")
importFrom(foreach,foreach)
importFrom(formatR,tidy_source)
importFrom(ggplot2,cut_interval)
importFrom(ggpubr,annotate_figure)
importFrom(ggpubr,as_ggplot)
importFrom(ggpubr,get_legend)
importFrom(ggpubr,ggarrange)
importFrom(ggpubr,ggtexttable)
importFrom(ggpubr,text_grob)
importFrom(ggpubr,theme_classic2)
importFrom(ggpubr,theme_pubr)
importFrom(ggpubr,ttheme)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,graphics.off)
importFrom(grDevices,pdf)
importFrom(grDevices,rainbow)
importFrom(graphics,abline)
importFrom(graphics,boxplot)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,text)
importFrom(gtools,mixedorder)
importFrom(gtools,mixedsort)
importFrom(iq,fast_MaxLFQ)
importFrom(limma,normalizeCyclicLoess)
importFrom(limma,squeezeVar)
importFrom(lme4,findbars)
importFrom(lme4,getME)
importFrom(lme4,lmerControl)
importFrom(lme4,refit)
importFrom(matrixStats,colMedians)
importFrom(matrixStats,rowMeans2)
importFrom(matrixStats,rowSds)
importFrom(matrixStats,rowSums2)
importFrom(missForest,missForest)
importFrom(msEmpiRe,normalize)
importFrom(openssl,md5)
importFrom(openxlsx,addWorksheet)
importFrom(openxlsx,createStyle)
importFrom(openxlsx,createWorkbook)
importFrom(openxlsx,read.xlsx)
importFrom(openxlsx,saveWorkbook)
importFrom(openxlsx,write.xlsx)
importFrom(openxlsx,writeData)
importFrom(pROC,coords)
importFrom(pROC,plot.roc)
importFrom(parallel,clusterExport)
importFrom(parallel,detectCores)
importFrom(parallel,makePSOCKcluster)
importFrom(parallel,stopCluster)
importFrom(patchwork,wrap_plots)
importFrom(pcaMethods,pca)
importFrom(pdftools,pdf_combine)
importFrom(purrr,imap)
importFrom(purrr,map)
importFrom(purrr,map_chr)
importFrom(purrr,map_lgl)
importFrom(readr,read_lines)
importFrom(rlang,":=")
importFrom(rlang,.data)
importFrom(rmarkdown,render)
importFrom(scales,percent_format)
importFrom(scales,rescale)
importFrom(stats,.lm.fit)
importFrom(stats,contrasts)
importFrom(stats,cov)
importFrom(stats,density)
importFrom(stats,ecdf)
importFrom(stats,loess)
importFrom(stats,mad)
importFrom(stats,median)
importFrom(stats,na.exclude)
importFrom(stats,na.omit)
importFrom(stats,optim)
importFrom(stats,p.adjust)
importFrom(stats,p.adjust.methods)
importFrom(stats,predict)
importFrom(stats,pt)
importFrom(stats,quantile)
importFrom(stats,resid)
importFrom(stats,residuals)
importFrom(stats,rt)
importFrom(stats,sd)
importFrom(stats,sigma)
importFrom(stats,weights)
importFrom(stringi,stri_sub_replace)
importFrom(stringr,str_count)
importFrom(stringr,str_split_fixed)
importFrom(stringr,str_squish)
importFrom(stringr,str_sub)
importFrom(stringr,str_trunc)
importFrom(stringr,str_wrap)
importFrom(styler,cache_deactivate)
importFrom(styler,style_text)
importFrom(tibble,as_tibble)
importFrom(tibble,enframe)
importFrom(tibble,rowid_to_column)
importFrom(tidyr,everything)
importFrom(tidyr,gather)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(tidyselect,any_of)
importFrom(utils,capture.output)
importFrom(utils,combn)
importFrom(utils,data)
importFrom(utils,head)
importFrom(utils,help)
importFrom(utils,packageVersion)
importFrom(utils,relist)
importFrom(utils,tail)
importFrom(variancePartition,fitExtractVarPartModel)
importFrom(variancePartition,plotVarPart)
importFrom(viridis,scale_fill_viridis)
importFrom(vsn,justvsn)
importFrom(xtable,xtable)