178 lines (176 with data), 5.0 kB

# Generated by roxygen2: do not edit by hand

export("%>%")
export(Combat_Normal)
export(Contrast_Venn)
export(DESeq2_analyze)
export(Wilcoxon_analyze)
export(add_boxplot)
export(add_new_tile_layer)
export(adjust_alpha_scale)
export(adjust_color_tone)
export(adjust_export_pathway)
export(circos_fruits)
export(combat_tumor)
export(compare_merge)
export(create_base_plot)
export(deg_filter)
export(drawLegends)
export(edgeR_analyze)
export(enrich_circo_bar)
export(enrich_polar_bubble)
export(enrichment_circlize)
export(enrichment_spiral_plots)
export(extract_descriptions_counts)
export(extract_ntop_pathways)
export(extract_positive_pathways)
export(facet_density_foldchange)
export(filter_diff_genes)
export(four_degs_venn)
export(gather_graph_edge)
export(gather_graph_node)
export(gene_color)
export(gene_highlights)
export(gene_map_pathway)
export(get_gtex_exp)
export(get_tcga_exp)
export(highlight_by_node)
export(highlight_genes)
export(limma_analyze)
export(log_transform)
export(merge_density_foldchange)
export(merge_gtex_tcga)
export(merge_id_position)
export(merge_method_color)
export(new_ggraph)
export(pathway_count)
export(pathway_description)
export(prep_deseq2)
export(prep_edgeR)
export(prep_limma)
export(prep_wilcoxon)
export(process_heatdata)
export(seek_gtex_organ)
export(selectPathways)
export(spiral_newrle)
importFrom(ComplexHeatmap,Legend)
importFrom(ComplexHeatmap,draw)
importFrom(ComplexHeatmap,packLegend)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,results)
importFrom(Hmisc,capitalize)
importFrom(circlize,chordDiagram)
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,inner_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,pull)
importFrom(dplyr,row_number)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,cpm)
importFrom(edgeR,estimateGLMCommonDisp)
importFrom(edgeR,estimateGLMTagwiseDisp)
importFrom(edgeR,estimateGLMTrendedDisp)
importFrom(edgeR,filterByExpr)
importFrom(edgeR,glmFit)
importFrom(edgeR,glmLRT)
importFrom(edgeR,topTags)
importFrom(geomtextpath,geom_textpath)
importFrom(ggVennDiagram,ggVennDiagram)
importFrom(ggalt,stat_xspline)
importFrom(ggdensity,geom_hdr)
importFrom(ggdensity,geom_hdr_rug)
importFrom(ggnewscale,new_scale)
importFrom(ggnewscale,new_scale_fill)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,alpha)
importFrom(ggplot2,annotate)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,coord_polar)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,expansion)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,labs)
importFrom(ggplot2,margin)
importFrom(ggplot2,scale_alpha_continuous)
importFrom(ggplot2,scale_color_brewer)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_gradient)
importFrom(ggplot2,scale_fill_identity)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_size)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,theme_void)
importFrom(ggplot2,unit)
importFrom(ggpubr,stat_cor)
importFrom(ggraph,geom_edge_diagonal)
importFrom(ggraph,geom_node_point)
importFrom(ggraph,geom_node_text)
importFrom(ggraph,ggraph)
importFrom(ggraph,node_angle)
importFrom(ggraph,scale_edge_colour_brewer)
importFrom(ggtree,aes)
importFrom(ggtree,geom_hilight)
importFrom(ggtree,geom_point2)
importFrom(grDevices,col2rgb)
importFrom(grDevices,convertColor)
importFrom(grDevices,rgb)
importFrom(graphics,strwidth)
importFrom(grid,gpar)
importFrom(grid,grid.roundrect)
importFrom(grid,grid.text)
importFrom(grid,pushViewport)
importFrom(grid,unit)
importFrom(grid,upViewport)
importFrom(grid,viewport)
importFrom(hrbrthemes,theme_ipsum)
importFrom(limma,contrasts.fit)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,topTable)
importFrom(magrittr,"%>%")
importFrom(rlang,.data)
importFrom(rlang,sym)
importFrom(spiralize,spiral_initialize)
importFrom(spiralize,spiral_rect)
importFrom(spiralize,spiral_text)
importFrom(spiralize,spiral_track)
importFrom(stats,as.formula)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,quantile)
importFrom(stats,wilcox.test)
importFrom(stringr,str_c)
importFrom(sva,ComBat_seq)
importFrom(tibble,as_tibble)
importFrom(tibble,column_to_rownames)
importFrom(tibble,tibble)
importFrom(tidygraph,tbl_graph)
importFrom(tidyr,unite)
importFrom(utils,head)
importFrom(utils,read.table)
importFrom(utils,tail)