NAMESPACE

# Generated by roxygen2: do not edit by hand

export("%>%")
export(annotate_data)
export(build_index)
export(deseq2_analysis)
export(edger_analysis)
export(limma_voom_analysis)
export(make_upset)
export(pathway_analysis)
export(read_salmon)
export(run_dea)
export(run_fastqc)
export(run_multiqc)
export(run_salmon)
export(run_tximport)
export(sanity_check)
export(trim_fastq)
import(GO.db)
import(ggplot2)
import(org.Hs.eg.db)
import(org.Mm.eg.db)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromTximport)
importFrom(DESeq2,counts)
importFrom(DESeq2,plotDispEsts)
importFrom(DESeq2,results)
importFrom(DESeq2,vst)
importFrom(RColorBrewer,brewer.pal)
importFrom(SummarizedExperiment,assay)
importFrom(UpSetR,upset)
importFrom(crayon,bold)
importFrom(crayon,green)
importFrom(crayon,italic)
importFrom(crayon,red)
importFrom(crayon,underline)
importFrom(crayon,yellow)
importFrom(data.table,fread)
importFrom(doParallel,registerDoParallel)
importFrom(dplyr,arrange)
importFrom(dplyr,as_tibble)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,cpm)
importFrom(edgeR,estimateDisp)
importFrom(edgeR,glmQLFit)
importFrom(edgeR,plotBCV)
importFrom(edgeR,scaleOffset)
importFrom(edgeR,topTags)
importFrom(foreach,"%dopar%")
importFrom(foreach,foreach)
importFrom(gage,gage)
importFrom(gage,go.gsets)
importFrom(gage,kegg.gsets)
importFrom(ggdendro,dendro_data)
importFrom(ggdendro,segment)
importFrom(ggdendro,theme_dendro)
importFrom(ggrepel,geom_label_repel)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,dev.off)
importFrom(grDevices,png)
importFrom(grid,gpar)
importFrom(grid,grid.draw)
importFrom(grid,grid.rect)
importFrom(grid,unit.pmax)
importFrom(gridExtra,arrangeGrob)
importFrom(gtable,gtable_add_cols)
importFrom(limma,contrasts.fit)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,makeContrasts)
importFrom(limma,topTable)
importFrom(limma,voom)
importFrom(lubridate,mdy)
importFrom(magrittr,"%>%")
importFrom(magrittr,set_colnames)
importFrom(magrittr,set_rownames)
importFrom(matrixStats,rowVars)
importFrom(parallel,detectCores)
importFrom(parallel,makeCluster)
importFrom(parallel,stopCluster)
importFrom(purrr,map)
importFrom(reshape2,melt)
importFrom(rjson,fromJSON)
importFrom(stats,as.dendrogram)
importFrom(stats,formula)
importFrom(stats,hclust)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,prcomp)
importFrom(stats,relevel)
importFrom(tools,file_path_sans_ext)
importFrom(tximport,summarizeToGene)
importFrom(tximport,tximport)
importFrom(utils,combn)
importFrom(utils,read.table)
importFrom(utils,write.table)
importFrom(viridis,scale_fill_viridis)