basePath	HTMLReport-class
basePath,HTMLReport-method	HTMLReport-class
BaseReport-class	BaseReportType-class
baseUrl	HTMLReport-class
baseUrl,HTMLReport-method	HTMLReport-class
connectionHandlers	ReportHandlers-class
CSVFile	CSVFile
CSVFile-class	CSVFile-class
custHeaderPanel	custHeaderPanel
DataPackage	DataPackage
DataPackage-class	DataPackage-class
dependencies	DataPackage-class
dependencies,DataPackage-method	DataPackage-class
dependencies<-	DataPackage-class
dependencies<-,DataPackage,character-method	DataPackage-class
fileHandlers	ReportHandlers-class
filename	filename-methods
filename,CSVFile-method	filename-methods
filename,HTMLReport-method	filename-methods
filename-methods	filename-methods
fileWIndexHandlers	ReportHandlers-class
finish	finish-methods
finish,DataPackage-method	finish-methods
finish,HTMLReport-method	finish-methods
finish,HTMLReportRef-method	finish-methods
finish-methods	finish-methods
HTMLReport	HTMLReportRef-class
HTMLReport-class	HTMLReport-class
HTMLReportRef-class	HTMLReportRef-class
knitrHandlers	ReportHandlers-class
Link	Link
Link,character-method	Link
Link,HTMLReportRef-method	Link
Link,list-method	Link
Link-methods	Link
makeOldHTMLReport	HTMLReport
mockRnaSeqData	mockRnaSeqData
modifyReportDF	addReportColumns-methods
modifyReportDF,ANY,ANY,ANY-method	addReportColumns-methods
modifyReportDF,ANY,ANY,DESeqDataSet-method	addReportColumns-methods
modifyReportDF,ANY,ANY,DESeqResults-method	addReportColumns-methods
modifyReportDF,ANY,ANY,DGEExact-method	addReportColumns-methods
modifyReportDF,ANY,ANY,DGELRT-method	addReportColumns-methods
modifyReportDF,ANY,ANY,GeneSet-method	addReportColumns-methods
modifyReportDF,ANY,ANY,GOHyperGResult-method	addReportColumns-methods
modifyReportDF,ANY,ANY,MArrayLM-method	addReportColumns-methods
modifyReportDF-methods	addReportColumns-methods
name	BaseReportType-class
name,BaseReport-method	BaseReportType-class
name<-,BaseReport,character-method	BaseReportType-class
name<-,CSVFile,character-method	CSVFile-class
name<-,HTMLReport,character-method	HTMLReport-class
objectToHTML	objectToHTML-methods
objectToHTML,ANY-method	objectToHTML-methods
objectToHTML,character-method	objectToHTML-methods
objectToHTML,data.frame-method	objectToHTML-methods
objectToHTML,ggbio-method	objectToHTML-methods
objectToHTML,ggplot-method	objectToHTML-methods
objectToHTML,recordedplot-method	objectToHTML-methods
objectToHTML,trellis-method	objectToHTML-methods
objectToHTML,XMLInternalNode-method	objectToHTML-methods
objectToHTML-methods	objectToHTML-methods
page	HTMLReport-class
page,HTMLReport-method	HTMLReport-class
page<-	HTMLReport-class
page<-,HTMLReport,character-method	HTMLReport-class
path	BaseReportType-class
path,BaseReport-method	BaseReportType-class
path,DataPackage-method	DataPackage-class
path,HTMLReport-method	HTMLReport-class
path,HTMLReportRef-method	HTMLReportRef-class
path,ReportHandlers-method	ReportHandlers-class
publish	publish-methods
publish,ANY,DataPackage-method	publish-methods
publish,ANY,HTMLReport-method	publish-methods
publish,ANY,HTMLReportRef-method	HTMLReportRef-class
publish,ANY,list-method	publish-methods
publish,character,DataPackage-method	publish-methods
publish,data.frame,CSVFile-method	publish-methods
publish,data.frame,DataPackage-method	publish-methods
publish,data.frame,HTMLReport-method	publish-methods
publish,data.frame,HTMLReportRef-method	publish-methods
publish,DESeqDataSet,HTMLReportRef-method	publish-methods
publish,DESeqResults,HTMLReportRef-method	publish-methods
publish,DGEExact,ANY-method	publish-methods
publish,DGEExact,HTMLReport-method	publish-methods
publish,DGEExact,HTMLReportRef-method	publish-methods
publish,DGELRT,ANY-method	publish-methods
publish,DGELRT,HTMLReport-method	publish-methods
publish,DGELRT,HTMLReportRef-method	publish-methods
publish,GeneSet,HTMLReport-method	publish-methods
publish,GeneSetCollection,ANY-method	publish-methods
publish,GeneSetCollection,HTMLReport-method	publish-methods
publish,GeneSetCollection,HTMLReportRef-method	publish-methods
publish,GOHyperGResult,ANY-method	publish-methods
publish,GOHyperGResult,HTMLReport-method	publish-methods
publish,GOHyperGResult,HTMLReportRef-method	publish-methods
publish,HTMLReport,HTMLReport-method	publish-methods
publish,HTMLReport,HTMLReportRef-method	publish-methods
publish,HyperGResultBase,HTMLReport-method	publish-methods
publish,HyperGResultBase,HTMLReportRef-method	publish-methods
publish,list,HTMLReport-method	publish-methods
publish,list,HTMLReportRef-method	publish-methods
publish,MArrayLM,ANY-method	publish-methods
publish,MArrayLM,HTMLReport-method	publish-methods
publish,MArrayLM,HTMLReportRef-method	publish-methods
publish,PFAMHyperGResult,ANY-method	publish-methods
publish,PFAMHyperGResult,HTMLReport-method	publish-methods
publish,PFAMHyperGResult,HTMLReportRef-method	publish-methods
publish,trellis,HTMLReport-method	publish-methods
publish,trellis,HTMLReportRef-method	publish-methods
publish-methods	publish-methods
readReport	readReport
reportDirectory	BaseReportType-class
reportDirectory,BaseReport-method	BaseReportType-class
reportDirectory<-	BaseReportType-class
reportDirectory<-,BaseReport,character-method	BaseReportType-class
ReportHandlers-class	ReportHandlers-class
reporting.theme	reporting.theme
reporting.theme.alternate	reporting.theme.alternate
shinyHandlers	ReportHandlers-class
show,BaseReport-method	BaseReportType-class
show,HTMLReport-method	HTMLReport-class
show,HTMLReportRef-method	HTMLReportRef-class
title	BaseReportType-class
title,BaseReport-method	BaseReportType-class
title<-	BaseReportType-class
title<-,BaseReport,character-method	BaseReportType-class
toReportDF	toReportDF-methods
toReportDF,ANY-method	toReportDF-methods
toReportDF,data.frame-method	toReportDF-methods
toReportDF,DESeqDataSet-method	toReportDF-methods
toReportDF,DESeqResults-method	toReportDF-methods
toReportDF,DGEExact-method	toReportDF-methods
toReportDF,DGELRT-method	toReportDF-methods
toReportDF,GeneSet-method	toReportDF-methods
toReportDF,GeneSetCollection-method	toReportDF-methods
toReportDF,GOHyperGResult-method	toReportDF-methods
toReportDF,MArrayLM-method	toReportDF-methods
toReportDF,PFAMHyperGResult-method	toReportDF-methods
toReportDF-methods	toReportDF-methods
url,HTMLReport-method	HTMLReport-class
validConnection	validConnection
[[,HTMLReportRef,ANY,ANY-method	HTMLReportRef-class
[[,HTMLReportRef,ANY-method	HTMLReportRef-class
[[<-,HTMLReportRef,ANY,ANY,ANY-method	HTMLReportRef-class
