ReportingTools: Tools for making reports in various formats

The ReportingTools software package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser such as Safari, or in other formats readable by programs such as Excel. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser. For more examples, please visit our site: http:// research-pub.gene.com/ReportingTools.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ReportingTools")
AuthorJason A. Hackney, Melanie Huntley, Jessica L. Larson, Christina Chaivorapol, Gabriel Becker, and Josh Kaminker
Bioconductor views DataRepresentation GO GeneSetEnrichment Microarray RNASeq Software Visualization
Date of publicationNone
MaintainerJason A. Hackney <hackney.jason@gene.com>, Gabriel Becker <becker.gabe@gene.com>, Jessica L. Larson <larson.jessica@gmail.com>
LicenseArtistic-2.0
Version2.16.0

View on Bioconductor

Functions

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

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R R/AllGenerics.R R/AllOldClasses.R R/DESeqFunctions.R R/DGEExact-methods.R R/DGELRT-methods.R R/GeneSetCollection-methods.R R/HTMLReport-methods.R R/HyperGResult-methods.R R/Link.R R/MArrayLM-methods.R R/ReportHandlers-method.R R/ReportHandlers.R R/Utilities.R R/accessor-methods.R R/addReportColumns-methods.R R/annotate.genes.R R/check.eg.ids.R R/data.frame-methods.R R/finish-methods.R R/genePagesFunctions.R R/getDefaultColumnClasses-methods.R R/grabScriptAndStyle.R R/htmlReportRef-methods.R R/internal.R R/makeDESeqDF.R R/methods.R R/objectToHTML-methods.R R/openPage.R R/plotting_functions.R R/publish-methods.R R/readReport.R R/refClasses.R R/shinyFunctions.R R/show-methods.R R/toReportDF-methods.R R/trellis-methods.R
build
build/vignette.rds
data
data/mockRnaSeqData.RData
inst
inst/CITATION
inst/doc
inst/doc/basicReportingTools.R
inst/doc/basicReportingTools.Rnw
inst/doc/basicReportingTools.pdf
inst/doc/csslib
inst/doc/csslib/bootstrap.css
inst/doc/csslib/images
inst/doc/csslib/images/glyphicons-halflings-white.png
inst/doc/csslib/images/glyphicons-halflings.png
inst/doc/csslib/images/sort_asc.png
inst/doc/csslib/images/sort_asc_disabled.png
inst/doc/csslib/images/sort_both.png
inst/doc/csslib/images/sort_desc.png
inst/doc/csslib/images/sort_desc_disabled.png
inst/doc/csslib/reprise.table.bootstrap.css
inst/doc/figuresknitrReport
inst/doc/figuresknitrReport/knitrReport-59999.pdf
inst/doc/figuresknitrReport/knitrReport-59999.png
inst/doc/figuresknitrReport/knitrReport-72776.pdf
inst/doc/figuresknitrReport/knitrReport-72776.png
inst/doc/jslib
inst/doc/jslib/bootstrap.js
inst/doc/jslib/jquery-1.8.0.min.js
inst/doc/jslib/jquery.dataTables-1.9.3.js
inst/doc/jslib/jquery.dataTables.columnFilter.js
inst/doc/jslib/jquery.dataTables.plugins.js
inst/doc/jslib/jquery.dataTables.reprise.js
inst/doc/knitr.R
inst/doc/knitr.Rmd
inst/doc/knitr.html
inst/doc/microarrayAnalysis.R
inst/doc/microarrayAnalysis.Rnw
inst/doc/microarrayAnalysis.pdf
inst/doc/rnaseqAnalysis.R
inst/doc/rnaseqAnalysis.Rnw
inst/doc/rnaseqAnalysis.pdf
inst/doc/shiny.R
inst/doc/shiny.Rnw
inst/doc/shiny.pdf
inst/examples
inst/examples/LinkTest.R inst/examples/clobberstart.R
inst/examples/customizeVignette.Rmd
inst/examples/doRMDtest.R
inst/examples/extensibility.Rmd
inst/examples/extensibilityTest.R inst/examples/indexTest.R inst/examples/inlineTest.R
inst/examples/knitrformattest.Rmd
inst/examples/marraylmtest.Rmd
inst/examples/pfamtest.Rmd
inst/examples/posInsertion.R
inst/examples/publishFlowchart.dia
inst/examples/publishFlowchart.svg
inst/examples/shinyExample
inst/examples/shinyExample/ReadMe.R inst/examples/shinyExample/server.R
inst/examples/shinyExample/shinystuff.Rproj
inst/examples/shinyExample/ui.R inst/examples/testDGEExact.R inst/examples/testDOM.R inst/examples/testMicro.R inst/examples/testReadReport.R
inst/examples/testRmd.Rmd
inst/extdata
inst/extdata/csslib
inst/extdata/csslib/bootstrap.css
inst/extdata/csslib/bootstrap.spruce.css
inst/extdata/csslib/images
inst/extdata/csslib/images/glyphicons-halflings-white.png
inst/extdata/csslib/images/glyphicons-halflings.png
inst/extdata/csslib/images/sort_asc.png
inst/extdata/csslib/images/sort_asc_disabled.png
inst/extdata/csslib/images/sort_both.png
inst/extdata/csslib/images/sort_desc.png
inst/extdata/csslib/images/sort_desc_disabled.png
inst/extdata/csslib/reprise.table.bootstrap.css
inst/extdata/csslib/reprise.table.css
inst/extdata/jslib
inst/extdata/jslib/bootstrap.js
inst/extdata/jslib/jquery-1.8.0.min.js
inst/extdata/jslib/jquery.dataTables-1.9.3.js
inst/extdata/jslib/jquery.dataTables.columnFilter.js
inst/extdata/jslib/jquery.dataTables.plugins.js
inst/extdata/jslib/jquery.dataTables.reprise.js
inst/unitTests
inst/unitTests/test_Annotation.R inst/unitTests/test_DESeqDataSet.R inst/unitTests/test_DESeqResults.R inst/unitTests/test_DataFrame.R inst/unitTests/test_GeneSets.R inst/unitTests/test_HyperGResults.R inst/unitTests/test_Link.R inst/unitTests/test_MArrayLM.R inst/unitTests/test_edgeR.R inst/unitTests/test_handlerConst.R inst/unitTests/test_knitr.R inst/unitTests/test_reportmanip.R inst/unitTests/test_testObjectCreation.R
man
man/BaseReportType-class.Rd man/CSVFile-class.Rd man/CSVFile.Rd man/DataPackage-class.Rd man/DataPackage.Rd man/HTMLReport-class.Rd man/HTMLReport.Rd
man/HTMLReportRef-class.rd
man/Link.Rd man/ReportHandlers-class.Rd man/addReportColumns-methods.Rd man/custHeaderPanel.Rd man/filename-methods.Rd man/finish-methods.Rd man/makeDESeqDF.Rd man/mockRnaSeqData.Rd man/objectToHTML-methods.Rd man/publish-methods.Rd man/readReport.Rd man/reporting.theme.Rd man/reporting.theme.alternate.Rd man/toReportDF-methods.Rd man/validConnection.Rd
tests
tests/runTests.R
vignettes
vignettes/basicReportingTools.Rnw
vignettes/html1.png
vignettes/html3.png
vignettes/html6.png
vignettes/html8.png
vignettes/knitr.Rmd
vignettes/microarray1.png
vignettes/microarray2.png
vignettes/microarray3.png
vignettes/microarray4.png
vignettes/microarray5.png
vignettes/microarray6.png
vignettes/microarrayAnalysis.Rnw
vignettes/rnaseq1.png
vignettes/rnaseq2.png
vignettes/rnaseq3.png
vignettes/rnaseq4.png
vignettes/rnaseq5.png
vignettes/rnaseqAnalysis.Rnw
vignettes/shiny.Rnw
vignettes/shiny.png

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