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NAMESPACE
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176 lines (175 loc) · 4.79 KB
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# Generated by roxygen2: do not edit by hand
export("%>%")
export(add_assay)
export(add_randna)
export(add_sign)
export(add_stats)
export(advanced_test)
export(aov_scale_phosR)
export(block_randomize)
export(center_substring)
export(clustered_heatmap)
export(colab_subset_df)
export(corr_plot)
export(filter_perseus)
export(fix_maxq_pig)
export(fragpipe_read_in)
export(gct_to_long)
export(genes_from_kegg)
export(get_coldata)
export(get_df_wide_append_assay)
export(get_network)
export(get_rowdata)
export(impute_DEP2)
export(impute_perseus)
export(isee_mini)
export(lars_volcano)
export(log2fc_to_fc)
export(long_test)
export(make_mini)
export(maxq_to_ppe)
export(merge_se)
export(module_barplot)
export(my_theme)
export(optimized_spectronaut_to_se)
export(phos_read_in_int)
export(phos_read_in_occ)
export(phospho_ora)
export(plot_antigen)
export(plot_antigen_missing)
export(plot_signalome_map)
export(prep_ksea)
export(prep_phosR)
export(prep_phosR_from_ppe)
export(prep_ssgsea2)
export(pubmed_query)
export(scatterPlot)
export(scopus_query)
export(se_GOE)
export(se_modify)
export(se_read_in)
export(se_to_isee)
export(se_volcano)
export(spectronaut_read_in)
export(spectronaut_to_se)
export(test_diff_phosR)
export(to_long)
export(to_pdf)
export(write_phos)
export(write_prot)
import(SummarizedExperiment)
import(dplyr)
import(ggplot2)
import(ggraph)
importFrom(BiocGenerics,cbind)
importFrom(BiocGenerics,colnames)
importFrom(BiocGenerics,rownames)
importFrom(BiocGenerics,unique)
importFrom(DEP2,get_df_wide)
importFrom(DEP2,make_se)
importFrom(DEP2,make_unique)
importFrom(DEP2,plot_heatmap)
importFrom(DEP2,theme_DEP1)
importFrom(DOSE,parse_ratio)
importFrom(DescTools,Closest)
importFrom(HybridMTest,row.oneway.anova)
importFrom(PhosR,PhosphoExperiment)
importFrom(PhosR,kinaseSubstratePred)
importFrom(PhosR,kinaseSubstrateScore)
importFrom(PhosR,matANOVA)
importFrom(PhosR,meanAbundance)
importFrom(PhosR,phosCollapse)
importFrom(PhosR,plotSignalomeMap)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,expand.grid)
importFrom(SingleCellExperiment,reducedDims)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(clusterProfiler,enrichGO)
importFrom(clusterProfiler,gseGO)
importFrom(clusterProfiler,simplify)
importFrom(cmapR,melt_gct)
importFrom(cmapR,parse_gctx)
importFrom(cmapR,write_gct)
importFrom(cowplot,plot_grid)
importFrom(digest,digest)
importFrom(dplyr,across)
importFrom(dplyr,distinct)
importFrom(dplyr,ends_with)
importFrom(dplyr,filter)
importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(dplyr,if_all)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_all)
importFrom(dplyr,n)
importFrom(dplyr,rename)
importFrom(dplyr,rename_all)
importFrom(dplyr,rename_with)
importFrom(dplyr,select)
importFrom(dplyr,summarize)
importFrom(dplyr,summarize_all)
importFrom(dplyr,ungroup)
importFrom(fdrtool,fdrtool)
importFrom(fdrtool,gcmlcm)
importFrom(forcats,fct_rev)
importFrom(gdata,cbindX)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_brewer)
importFrom(ggplot2,scale_fill_discrete)
importFrom(ggplot2,scale_fill_viridis_d)
importFrom(ggplot2,sym)
importFrom(ggplot2,theme)
importFrom(ggpubr,stat_cor)
importFrom(ggrepel,geom_label_repel)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,colorRampPalette)
importFrom(iSEE,iSEE)
importFrom(iSEEu,registerFeatureSetCollections)
importFrom(iSEEu,registerLogFCPatterns)
importFrom(iSEEu,registerPValuePatterns)
importFrom(igraph,degree)
importFrom(igraph,delete.vertices)
importFrom(igraph,graph_from_data_frame)
importFrom(janitor,clean_names)
importFrom(janitor,make_clean_names)
importFrom(limma,contrasts.fit)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,makeContrasts)
importFrom(limma,topTable)
importFrom(magrittr,"%>%")
importFrom(patchwork,plot_annotation)
importFrom(patchwork,plot_layout)
importFrom(patchwork,wrap_plots)
importFrom(plyr,colwise)
importFrom(purrr,map_df)
importFrom(qvalue,qvalue)
importFrom(rbioapi,rba_string_interaction_partners)
importFrom(rbioapi,rba_string_interactions_network)
importFrom(rbioapi,rba_string_map_ids)
importFrom(rlang,"!!")
importFrom(splitstackshape,cSplit)
importFrom(stats,cor.test)
importFrom(stats,model.matrix)
importFrom(stats,p.adjust)
importFrom(stats,prcomp)
importFrom(stringr,str_wrap)
importFrom(tibble,column_to_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,gather)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,unite)
importFrom(tidyselect,ends_with)
importFrom(vroom,vroom)