NAMESPACE

# Generated by roxygen2: do not edit by hand

export("aln_metrics<-")
export("de_results<-")
export("dgelist<-")
export("edger<-")
export("norm_cts<-")
export(BbcEdgeR)
export(BbcSE)
export(aln_metrics)
export(batch_correct_norm_cts)
export(de_results)
export(deseq2)
export(dgelist)
export(edger)
export(ens2entrez)
export(ens2sym)
export(findDEGs)
export(find_missing_in_gseaResult)
export(get_de_table)
export(lists_to_edger_contrasts)
export(makeDGEList)
export(norm_cts)
export(normalize_counts)
export(plot_PCA)
export(plot_aln_metrics)
export(plot_heatmap)
export(plot_pval_distrib)
export(plot_volcano)
export(prep_clusterprofiler_genelist)
export(read_col_meta)
export(read_star_aln_metrics)
export(run_gsea)
export(run_hypergeometric)
export(searchBM)
export(shorten_desc)
export(star_to_mat)
exportMethods("[")
exportMethods("[<-")
exportMethods(cbind)
exportMethods(findDEGs)
exportMethods(normalize_counts)
exportMethods(rbind)
exportMethods(run_gsea)
exportMethods(run_hypergeometric)
exportMethods(shorten_desc)
exportMethods(show)
import(SummarizedExperiment)
import(ggplot2)
importClassesFrom(DESeq2,DESeqDataSet)
importClassesFrom(SummarizedExperiment,Assays)
importClassesFrom(SummarizedExperiment,SummarizedExperiment)
importClassesFrom(edgeR,DGEExact)
importClassesFrom(edgeR,DGEGLM)
importClassesFrom(edgeR,DGELRT)
importClassesFrom(edgeR,DGEList)
importFrom(AnnotationDbi,keys)
importFrom(AnnotationDbi,keytypes)
importFrom(AnnotationDbi,mapIds)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(DOSE,setReadable)
importFrom(EnhancedVolcano,EnhancedVolcano)
importFrom(GenomicRanges,GRanges)
importFrom(RColorBrewer,brewer.pal)
importFrom(ReactomePA,enrichPathway)
importFrom(ReactomePA,gsePathway)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,metadata)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,colData)
importFrom(biomaRt,getBM)
importFrom(biomaRt,listDatasets)
importFrom(biomaRt,useDataset)
importFrom(biomaRt,useMart)
importFrom(circlize,colorRamp2)
importFrom(clusterProfiler,GSEA)
importFrom(clusterProfiler,enrichGO)
importFrom(clusterProfiler,enrichKEGG)
importFrom(clusterProfiler,enricher)
importFrom(clusterProfiler,gseKEGG)
importFrom(cowplot,theme_cowplot)
importFrom(dplyr,across)
importFrom(dplyr,arrange)
importFrom(dplyr,ends_with)
importFrom(dplyr,filter)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,cpm)
importFrom(edgeR,estimateDisp)
importFrom(edgeR,filterByExpr)
importFrom(edgeR,glmQLFTest)
importFrom(edgeR,glmQLFit)
importFrom(edgeR,glmTreat)
importFrom(edgeR,topTags)
importFrom(limma,makeContrasts)
importFrom(limma,nonEstimable)
importFrom(limma,removeBatchEffect)
importFrom(magrittr,"%>%")
importFrom(methods,as)
importFrom(methods,callNextMethod)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,slotNames)
importFrom(methods,validObject)
importFrom(msigdbr,msigdbr)
importFrom(readr,read_tsv)
importFrom(rlang,.data)
importFrom(stats,as.formula)
importFrom(stats,complete.cases)
importFrom(stats,model.matrix)
importFrom(stats,prcomp)
importFrom(stringr,str_detect)
importFrom(stringr,str_remove)
importFrom(stringr,str_replace)
importFrom(stringr,str_trunc)
importFrom(testthat,expect_warning)
importFrom(tibble,as_tibble)
importFrom(tibble,column_to_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tidyselect,ends_with)
importFrom(utils,capture.output)
importFrom(vegan,adonis)
importFrom(vegan,vegdist)
importMethodsFrom(SummarizedExperiment,rbind)
importMethodsFrom(SummarizedExperiment,show)