importClassesFrom(Category, HyperGResultBase, PFAMHyperGResult)
importClassesFrom(GOstats, GOHyperGResult)
importClassesFrom(Biobase, ExpressionSet)
importClassesFrom(limma, MArrayLM)
importClassesFrom(edgeR, DGEExact, DGELRT, DGEList)
importClassesFrom(GSEABase, GeneSetCollection)
importClassesFrom(DESeq2, DESeqDataSet, DESeqResults)
#importClassesFrom(ggbio, GGbio)

importFrom(annotate, getAnnMap, annPkgName)
importFrom(limma, topTable)
importFrom(grid, grid.newpage, viewport, pushViewport, upViewport, unit)
importFrom(edgeR, topTags, cpm)
importFrom(GOstats, termGraphs, inducedTermGraph, plotGOTermGraph)
importFrom(DESeq2, results, resultsNames)
importFrom(ggplot2, ggplot) #we don't actually need this, we just need to be able to do setOldClass and have ggplot2 listed in imports

importMethodsFrom(AnnotationDbi, select, summary, mget)
importMethodsFrom(Category, summary, geneIdsByCategory, geneIdUniverse)
importMethodsFrom(GOstats, summary)
importMethodsFrom(GSEABase, geneIds, geneIdType)
importMethodsFrom(XML, '[[')
importMethodsFrom(IRanges, as.data.frame)

import(methods)
import(knitr)
import(BiocGenerics)
import(ggbio) #we should only be importing the GGbio class, but it isn't exported properly.

import(lattice)
import(PFAM.db)
importFrom(R.utils, getRelativePath) #this is a lot of dependencies for one function
importFrom(hwriter, openPage, hwrite, closePage, hwriteImage, hmakeTag)
importFrom(XML, htmlParse, getNodeSet, saveXML, xmlRoot, addChildren,
    newXMLNode, removeChildren, xmlChildren, xmlValue, xmlAttrs, 'xmlValue<-',
    addSibling, xpathSApply)

export(HTMLReport, CSVFile, DataPackage, validConnection,
    reporting.theme.alternate, reporting.theme, makeDESeqDF, readReport,
    fileHandlers, connectionHandlers, knitrHandlers, shinyHandlers,
    fileWIndexHandlers, makeOldHTMLReport, custHeaderPanel)
exportMethods(publish, name, title, 'title<-', reportDirectory,
    'reportDirectory<-', filename, path, url, page, 'page<-', finish, show,
    basePath, baseUrl, dependencies, "dependencies<-", modifyReportDF,
    objectToHTML, toReportDF, Link)
exportClasses(DataPackage, CSVFile, HTMLReport, BaseReport, HTMLReportRef, 
    ReportHandlers)