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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export("assay<-")
export("colData<-")
export("metadata<-")
export("rowData<-")
export(GN_normalization)
export(GSEA_test)
export(Heatmap)
export(HeatmapAnnotation)
export(MD_normalization)
export(PSM_barplot)
export(PTM_normalization)
export(VSN_normalization)
export(add_rejections)
export(assay)
export(average_samples)
export(bar_number)
export(colData)
export(consensus_clustering_analysis)
export(get_cluster_heatmap)
export(get_density)
export(glycoPSM_barplot)
export(impute)
export(make_se_customized)
export(make_se_from_files)
export(make_unique)
export(manual_impute)
export(metadata)
export(or_test)
export(plot_GSEA)
export(plot_correlation_heatmap)
export(plot_cvs)
export(plot_feature)
export(plot_feature_numbers)
export(plot_glycan_distribution)
export(plot_missval_heatmap)
export(plot_or)
export(plot_pca)
export(plot_peptide_volcano)
export(plot_volcano)
export(prepare_PTMSEA)
export(prepare_kinome)
export(readResultRData)
export(remove_samples)
export(rowData)
export(snf_analysis)
export(test_diff)
export(test_limma)
export(visualize_PTMSEA)
export(visualize_kinome)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,draw)
importFrom(ComplexHeatmap,row_order)
importFrom(ConsensusClusterPlus,ConsensusClusterPlus)
importFrom(MSnbase,MSnSet)
importFrom(RColorBrewer,brewer.pal)
importFrom(RColorBrewer,brewer.pal.info)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,metadata)
importFrom(SNFtool,SNF)
importFrom(SNFtool,affinityMatrix)
importFrom(SNFtool,dist2)
importFrom(SNFtool,spectralClustering)
importFrom(SNFtool,standardNormalization)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(clusterProfiler,GSEA)
importFrom(cmapR,GCT)
importFrom(cmapR,ids)
importFrom(cmapR,mat)
importFrom(cmapR,meta)
importFrom(cmapR,parse_gctx)
importFrom(dplyr,all_of)
importFrom(dplyr,arrange)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,recode)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(dplyr,summarise)
importFrom(dplyr,summarise_if)
importFrom(dplyr,summarize)
importFrom(fdrtool,fdrtool)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_jitter)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_colorbar)
importFrom(ggplot2,labs)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,scale_color_brewer)
importFrom(ggplot2,scale_color_continuous)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_size_continuous)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,colorRampPalette)
importFrom(grid,gpar)
importFrom(grid,unit)
importFrom(httr,GET)
importFrom(limma,contrasts.fit)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,makeContrasts)
importFrom(limma,topTable)
importFrom(magrittr,"%>%")
importFrom(matrixStats,colMedians)
importFrom(plotly,add_trace)
importFrom(plotly,layout)
importFrom(plotly,plot_ly)
importFrom(purrr,map_df)
importFrom(readr,parse_factor)
importFrom(stringr,str_count)
importFrom(tibble,column_to_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,gather)
importFrom(tidyr,spread)
importFrom(tidyr,unite)
importFrom(vsn,predict)
importFrom(vsn,vsnMatrix)