Package: ReportingTools 2.47.0

Jason A. Hackney

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.

Authors:Jason A. Hackney, Melanie Huntley, Jessica L. Larson, Christina Chaivorapol, Gabriel Becker, and Josh Kaminker

ReportingTools_2.47.0.tar.gz
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ReportingTools.pdf |ReportingTools.html✨
ReportingTools/json (API)
NEWS

# Install 'ReportingTools' in R:
install.packages('ReportingTools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On BioConductor:ReportingTools-2.47.0(bioc 3.21)ReportingTools-2.46.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncologysoftwarevisualizationmicroarrayrnaseqgodatarepresentationgenesetenrichment

6.23 score 1 packages 93 scripts 1.3k downloads 6 mentions 35 exports 173 dependencies

Last updated 4 months agofrom:30a7956038. Checks:1 OK, 7 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 20 2025
R-4.5-winNOTEFeb 20 2025
R-4.5-macNOTEFeb 20 2025
R-4.5-linuxNOTEFeb 20 2025
R-4.4-winNOTEFeb 20 2025
R-4.4-macNOTEFeb 20 2025
R-4.3-winNOTEFeb 20 2025
R-4.3-macNOTEFeb 20 2025

Exports:basePathbaseUrlconnectionHandlersCSVFilecustHeaderPanelDataPackagedependenciesdependencies<-fileHandlersfilenamefileWIndexHandlersfinishHTMLReportknitrHandlersLinkmakeOldHTMLReportmodifyReportDFnameobjectToHTMLpagepage<-pathpublishreadReportreportDirectoryreportDirectory<-reporting.themereporting.theme.alternateshinyHandlersshowtitletitle<-toReportDFurlvalidConnection

Dependencies:abindannotateAnnotationDbiAnnotationFilterAnnotationForgeaskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemCategorycheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArrayDESeq2dichromatdigestdplyredgeRensembldbevaluatefansifarverfastmapfilelockfontawesomeforcatsforeignformatRFormulafsfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGGallyggbioggplot2ggstatsglueGO.dbGOstatsgraphgridExtraGSEABasegtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2hwriterIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslOrganismDbipatchworkPFAM.dbpillarpkgconfigplogrplyrpngprettyunitsprogressProtGenericspurrrR.methodsS3R.ooR.utilsR6rappdirsRBGLRColorBrewerRcppRcppArmadilloRCurlreshape2restfulrRgraphvizRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytextxdbmakerUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2xtableXVectoryaml

Reporting on microarray differential expression

Rendered frommicroarrayAnalysis.Rnwusingutils::Sweaveon Feb 20 2025.

Last update: 2016-12-04
Started: 2012-09-20

Reporting on RNA-seq differential expression

Rendered fromrnaseqAnalysis.Rnwusingutils::Sweaveon Feb 20 2025.

Last update: 2020-11-30
Started: 2012-09-20

ReportingTools basics

Rendered frombasicReportingTools.Rnwusingutils::Sweaveon Feb 20 2025.

Last update: 2014-04-03
Started: 2012-09-20

ReportingTools shiny

Rendered fromshiny.Rnwusingutils::Sweaveon Feb 20 2025.

Last update: 2014-04-03
Started: 2013-03-18

Readme and manuals

Help Manual

Help pageTopics
Class '"BaseReport"'BaseReport-class name name,BaseReport-method name<-,BaseReport,character-method path path,BaseReport-method reportDirectory reportDirectory,BaseReport-method reportDirectory<- reportDirectory<-,BaseReport,character-method show,BaseReport-method title title,BaseReport-method title<- title<-,BaseReport,character-method
Function for creating and initializing a CSVFile for publishing resultsCSVFile
Class '"CSVFile"'CSVFile-class name<-,CSVFile,character-method
Define a header panel with custom JS/CSS for a Shiny appcustHeaderPanel
Function for creating and initializing an object of class DataPackage.DataPackage
Class '"DataPackage"'DataPackage-class dependencies dependencies,DataPackage-method dependencies<- dependencies<-,DataPackage,character-method path,DataPackage-method
Methods for getting the name of a file for a CSVFile or HTMLReport.filename filename,CSVFile-method filename,HTMLReport-method filename-methods
Finalizing reports after publishing resultsfinish finish,DataPackage-method finish,HTMLReport-method finish,HTMLReportRef-method finish-methods
Class '"HTMLReport"'basePath basePath,HTMLReport-method baseUrl baseUrl,HTMLReport-method HTMLReport-class name<-,HTMLReport,character-method page page,HTMLReport-method page<- page<-,HTMLReport,character-method path,HTMLReport-method show,HTMLReport-method url,HTMLReport-method
Class '"HTMLReportRef"'HTMLReport HTMLReportRef-class path,HTMLReportRef-method publish,ANY,HTMLReportRef-method show,HTMLReportRef-method [[,HTMLReportRef,ANY,ANY-method [[,HTMLReportRef,ANY-method [[<-,HTMLReportRef,ANY,ANY,ANY-method
Create a table of LinksLink Link,character-method Link,HTMLReportRef-method Link,list-method Link-methods
Creating and initializing an HTMLReport objectmakeOldHTMLReport
A counts table of mock RNA-deq data in mouse.mockRnaSeqData
Decorate the Basic data.frame Representation of an ObjectmodifyReportDF modifyReportDF,ANY,ANY,ANY-method modifyReportDF,ANY,ANY,DESeqDataSet-method modifyReportDF,ANY,ANY,DESeqResults-method modifyReportDF,ANY,ANY,DGEExact-method modifyReportDF,ANY,ANY,DGELRT-method modifyReportDF,ANY,ANY,GeneSet-method modifyReportDF,ANY,ANY,GOHyperGResult-method modifyReportDF,ANY,ANY,MArrayLM-method modifyReportDF-methods
Transform R objects into HTML form to be inserted in HTML reportsobjectToHTML objectToHTML,ANY-method objectToHTML,character-method objectToHTML,data.frame-method objectToHTML,ggbio-method objectToHTML,ggplot-method objectToHTML,recordedplot-method objectToHTML,trellis-method objectToHTML,XMLInternalNode-method objectToHTML-methods
Methods for publishing a variety of data types in selected output formatspublish publish,ANY,DataPackage-method publish,ANY,HTMLReport-method publish,ANY,list-method publish,character,DataPackage-method publish,data.frame,CSVFile-method publish,data.frame,DataPackage-method publish,data.frame,HTMLReport-method publish,data.frame,HTMLReportRef-method publish,DESeqDataSet,HTMLReportRef-method publish,DESeqResults,HTMLReportRef-method publish,DGEExact,ANY-method publish,DGEExact,HTMLReport-method publish,DGEExact,HTMLReportRef-method publish,DGELRT,ANY-method publish,DGELRT,HTMLReport-method publish,DGELRT,HTMLReportRef-method publish,GeneSet,HTMLReport-method publish,GeneSetCollection,ANY-method publish,GeneSetCollection,HTMLReport-method publish,GeneSetCollection,HTMLReportRef-method publish,GOHyperGResult,ANY-method publish,GOHyperGResult,HTMLReport-method publish,GOHyperGResult,HTMLReportRef-method publish,HTMLReport,HTMLReport-method publish,HTMLReport,HTMLReportRef-method publish,HyperGResultBase,HTMLReport-method publish,HyperGResultBase,HTMLReportRef-method publish,list,HTMLReport-method publish,list,HTMLReportRef-method publish,MArrayLM,ANY-method publish,MArrayLM,HTMLReport-method publish,MArrayLM,HTMLReportRef-method publish,PFAMHyperGResult,ANY-method publish,PFAMHyperGResult,HTMLReport-method publish,PFAMHyperGResult,HTMLReportRef-method publish,trellis,HTMLReport-method publish,trellis,HTMLReportRef-method publish-methods
Read in an Existing ReportreadReport
Class '"ReportHandlers"'connectionHandlers fileHandlers fileWIndexHandlers knitrHandlers path,ReportHandlers-method ReportHandlers-class shinyHandlers
Color theme for use in ReportingToolsreporting.theme
Alternate color theme for use in ReportingToolsreporting.theme.alternate
Class Specific Default Behavior for Transforming Objects to data.framestoReportDF toReportDF,ANY-method toReportDF,data.frame-method toReportDF,DESeqDataSet-method toReportDF,DESeqResults-method toReportDF,DGEExact-method toReportDF,DGELRT-method toReportDF,GeneSet-method toReportDF,GeneSetCollection-method toReportDF,GOHyperGResult-method toReportDF,MArrayLM-method toReportDF,PFAMHyperGResult-method toReportDF-methods
Determine connection validityvalidConnection