Introduction | Differential expression analysis with edgeR | Differential expression analysis with DESeq2 | GO analysis using GOstats | PFAM analysis | Putting it all together | References
Package: ReportingTools 2.53.0
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:
ReportingTools_2.53.0.tar.gz
ReportingTools_2.53.0.zip(r-4.7)ReportingTools_2.53.0.zip(r-4.6)ReportingTools_2.53.0.zip(r-4.5)
ReportingTools_2.53.0.tgz(r-4.6-any)ReportingTools_2.53.0.tgz(r-4.5-any)
ReportingTools_2.53.0.tar.gz(r-4.7-any)ReportingTools_2.53.0.tar.gz(r-4.6-any)
ReportingTools_2.53.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ReportingTools/json (API)
| # Install 'ReportingTools' in R: |
| install.packages('ReportingTools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- mockRnaSeqData - A counts table of mock RNA-deq data in mouse.
On BioConductor:ReportingTools-2.53.0(bioc 3.24)ReportingTools-2.52.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologysoftwarevisualizationmicroarrayrnaseqgodatarepresentationgenesetenrichment
Last updated from:fe3989bf31. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 349 | ||
| linux-devel-x86_64 | NOTE | 739 | ||
| source / vignettes | OK | 463 | ||
| linux-release-x86_64 | NOTE | 746 | ||
| macos-release-arm64 | NOTE | 578 | ||
| macos-oldrel-arm64 | NOTE | 452 | ||
| windows-devel | NOTE | 786 | ||
| windows-release | NOTE | 808 | ||
| windows-oldrel | NOTE | 841 | ||
| wasm-release | OK | 293 |
Exports:basePathbaseUrlconnectionHandlersCSVFilecustHeaderPanelDataPackagedependenciesdependencies<-fileHandlersfilenamefileWIndexHandlersfinishHTMLReportknitrHandlersLinkmakeOldHTMLReportmodifyReportDFnameobjectToHTMLpagepage<-pathpublishreadReportreportDirectoryreportDirectory<-reporting.themereporting.theme.alternateshinyHandlersshowtitletitle<-toReportDFurlvalidConnection
Dependencies:abindannotateAnnotationDbiAnnotationFilterAnnotationForgeaskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemCategorycheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArrayDESeq2dichromatdigestedgeRensembldbevaluatefarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggbioggplot2glueGO.dbGOstatsgraphgridExtraGSEABasegtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrhwriterIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslOrganismDbiPFAM.dbpkgconfigplyrpngProtGenericsR.methodsS3R.ooR.utilsR6rappdirsRBGLRColorBrewerRcppRcppArmadilloRCurlreshape2restfulrRgraphvizRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystinytexUCSC.utilsVariantAnnotationvctrsviridisLitewithrxfunXMLxtableXVectoryaml
Reporting on RNA-seq differential expression
Last update: 2020-11-30
Started: 2012-09-20
Reporting on microarray differential expression
Introduction | Differential expression analysis using limma | GO analysis using GOstats | PFAM analysis | GSEA analysis | Putting it all together | References
Last update: 2016-12-04
Started: 2012-09-20
ReportingTools basics
Introduction | Basics of Reporting | Adding plots or text to a report | Adding plots or links to a report table | Multiple Tables to the same page | Publishing other types of data and more advanced features | References
Last update: 2014-04-03
Started: 2012-09-20
ReportingTools shiny
Introduction | Changes to ui.R when using ReportingTools | Changes to server.R when using ReportingTools | References
Last update: 2014-04-03
Started: 2013-03-18
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 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 results | CSVFile |
| Class '"CSVFile"' | CSVFile-class name<-,CSVFile,character-method |
| Define a header panel with custom JS/CSS for a Shiny app | custHeaderPanel |
| 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 results | finish 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 Links | Link Link,character-method Link,HTMLReportRef-method Link,list-method Link-methods |
| Creating and initializing an HTMLReport object | makeOldHTMLReport |
| A counts table of mock RNA-deq data in mouse. | mockRnaSeqData |
| Decorate the Basic data.frame Representation of an Object | modifyReportDF 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 reports | objectToHTML 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 formats | publish 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 Report | readReport |
| Class '"ReportHandlers"' | connectionHandlers fileHandlers fileWIndexHandlers knitrHandlers path,ReportHandlers-method ReportHandlers-class shinyHandlers |
| Color theme for use in ReportingTools | reporting.theme |
| Alternate color theme for use in ReportingTools | reporting.theme.alternate |
| Class Specific Default Behavior for Transforming Objects to data.frames | toReportDF 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 validity | validConnection |
