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.

Author
Jason A. Hackney, Melanie Huntley, Jessica L. Larson, Christina Chaivorapol, Gabriel Becker, and Josh Kaminker
Date of publication
None
Maintainer
Jason A. Hackney <hackney.jason@gene.com>, Gabriel Becker <becker.gabe@gene.com>, Jessica L. Larson <larson.jessica@gmail.com>
License
Artistic-2.0
Version
2.14.0

View on Bioconductor

Man pages

addReportColumns-methods
Decorate the Basic data.frame Representation of an Object
BaseReportType-class
Class '"BaseReport"'
CSVFile
Function for creating and initializing a CSVFile for...
CSVFile-class
Class '"CSVFile"'
custHeaderPanel
Define a header panel with custom JS/CSS for a Shiny app
DataPackage
Function for creating and initializing an object of class...
DataPackage-class
Class '"DataPackage"'
filename-methods
Methods for getting the name of a file for a CSVFile or...
finish-methods
Finalizing reports after publishing results
HTMLReport
Creating and initializing an HTMLReport object
HTMLReport-class
Class '"HTMLReport"'
Link
Create a table of Links
makeDESeqDF
Converts DESeq results into a data frame to be published
mockRnaSeqData
A counts table of mock RNA-deq data in mouse.
objectToHTML-methods
Transform R objects into HTML form to be inserted in HTML...
publish-methods
Methods for publishing a variety of data types in selected...
readReport
Read in an Existing Report
ReportHandlers-class
Class '"ReportHandlers"'
reporting.theme
Color theme for use in ReportingTools
reporting.theme.alternate
Alternate color theme for use in ReportingTools
toReportDF-methods
Class Specific Default Behavior for Transforming Objects to...
validConnection
Determine connection validity

Files in this package

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