NAMESPACE

# Generated by roxygen2: do not edit by hand

export(blue.colors)
export(concatenate_by_features)
export(correct_batch_effect)
export(correct_batch_effect_empiricalBayesLM)
export(dist)
export(dusk.colors)
export(eset_lm)
export(eset_presence_absence)
export(exhaustive_ratios)
export(heatmap.3)
export(heatmap.plus.2)
export(hot.colors)
export(hot2.colors)
export(image_msnset)
export(jet.colors)
export(jet2.colors)
export(keep_longest_isoform_per_gene)
export(knn_imputation)
export(limma_a_b)
export(limma_gen)
export(lr_modeling)
export(lsos)
export(make.unique.2)
export(map_PTM_sites)
export(mixed_effects_anova)
export(msnset2txt)
export(normalizeByGlob)
export(normalizeByRef)
export(normalize_by_feature_property)
export(plotAUC)
export(plot_annHeatmap2)
export(plot_feature)
export(plot_pca_v1)
export(plot_pca_v2)
export(plot_pca_v3)
export(plot_pca_v4)
export(plot_umap)
export(protein_inference)
export(readMaxQuantPeptides)
export(readMaxQuantProtGroups)
export(readMaxQuantSummary)
export(readSkyLinePRR)
export(remove_batch_effect)
export(remove_covariate)
export(rf_modeling)
export(rrollup)
export(subset_by_size)
export(volcano_plot)
export(xtable2)
import(Boruta)
import(glmnet)
import(qvalue)
import(randomForest)
import(umap)
import(varSelRF)
importClassesFrom(Matrix,dgCMatrix)
importFrom(Biobase,exprs)
importFrom(Biobase,fData)
importFrom(Biobase,featureNames)
importFrom(Biobase,pData)
importFrom(BiocParallel,bpparam)
importFrom(FField,FFieldPtRep)
importFrom(MSnbase,MSnSet)
importFrom(RColorBrewer,"brewer.pal")
importFrom(ROCR,performance)
importFrom(ROCR,prediction)
importFrom(WGCNA,empiricalBayesLM)
importFrom(ade4,"dudi.pca")
importFrom(data.table,rbindlist)
importFrom(data.table,setDT)
importFrom(doParallel,registerDoParallel)
importFrom(dplyr,arrange)
importFrom(dplyr,case_when)
importFrom(dplyr,do)
importFrom(dplyr,filter)
importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(dplyr,group_by_at)
importFrom(dplyr,inner_join)
importFrom(dplyr,matches)
importFrom(dplyr,mutate)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,row_number)
importFrom(dplyr,select)
importFrom(dplyr,semi_join)
importFrom(dplyr,summarize)
importFrom(foreach,"%dopar%")
importFrom(foreach,foreach)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_raster)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_fill_gradient2)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,stat_ellipse)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(ggrepel,geom_label_repel)
importFrom(gplots,bluered)
importFrom(gplots,heatmap.2)
importFrom(grid,unit)
importFrom(iterators,icount)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,topTable)
importFrom(lme4,lmer)
importFrom(magrittr,"%>%")
importFrom(outliers,grubbs.test)
importFrom(outliers,outlier)
importFrom(parallel,detectCores)
importFrom(parallel,makeCluster)
importFrom(parallel,mclapply)
importFrom(parallel,stopCluster)
importFrom(pcaMethods,pca)
importFrom(plyr,ddply)
importFrom(purrr,map)
importFrom(purrr,map2)
importFrom(qvalue,qvalue)
importFrom(reshape2,melt)
importFrom(rlang,"!!")
importFrom(rlang,":=")
importFrom(rlang,parse_expr)
importFrom(scales,log_breaks)
importFrom(scales,pretty_breaks)
importFrom(scales,rescale)
importFrom(scales,trans_new)
importFrom(stringr,str_detect)
importFrom(stringr,str_length)
importFrom(stringr,str_locate_all)
importFrom(stringr,str_replace_all)
importFrom(stringr,str_sub)
importFrom(stringr,str_wrap)
importFrom(sva,ComBat)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,gather)
importFrom(tidyselect,one_of)
importFrom(xtable,print.xtable)
importFrom(xtable,xtable)