Package: ReportingTools 2.45.0

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_2.45.0.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:

mockRnaSeqData - A counts table of mock RNA-deq data in mouse.

On BioConductor:ReportingTools-2.45.0(bioc 3.20)ReportingTools-2.44.0(bioc 3.19)

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

bioconductor-package

35 exports 2.53 score 182 dependencies 2 dependents 6 mentions

Last updated 2 months agofrom:1690137e90

Exports:basePath baseUrl connectionHandlers CSVFile custHeaderPanel DataPackage dependencies dependencies<-fileHandlers filename fileWIndexHandlers finish HTMLReport knitrHandlers Link makeOldHTMLReport modifyReportDF name objectToHTML page page<-path publish readReport reportDirectory reportDirectory<-reporting.theme reporting.theme.alternate shinyHandlers show title title<-toReportDF url validConnection

Dependencies:abind annotate AnnotationDbi AnnotationFilter AnnotationForge askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob broom broom.helpers BSgenome bslib cachem Category checkmate cli clipr cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray DESeq2 dichromat digest dplyr edgeR ensembldb evaluate fansi farver fastmap filelock fontawesome forcats foreign formatR Formula fs futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GGally ggbio ggplot2 ggstats glue GO.db GOstats graph gridExtra GSEABase gtable haven highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 hwriter IRanges isoband jquerylib jsonlite KEGGREST knitr labeling labelled lambda.r lattice lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl OrganismDbi patchwork PFAM.db pillar pkgconfig plogr plyr png prettyunits progress ProtGenerics purrr R.methodsS3 R.oo R.utils R6 rappdirs RBGL RColorBrewer Rcpp RcppArmadillo RCurl readr reshape2 restfulr Rgraphviz Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex txdbmaker tzdb UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite vroom withr xfun XML xml2 xtable XVector yaml zlibbioc

Reporting on microarray differential expression

Rendered frommicroarrayAnalysis.Rnwusingutils::Sweaveon Jul 04 2024.

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

Reporting on RNA-seq differential expression

Rendered fromrnaseqAnalysis.Rnwusingutils::Sweaveon Jul 04 2024.

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

ReportingTools basics

Rendered frombasicReportingTools.Rnwusingutils::Sweaveon Jul 04 2024.

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

ReportingTools shiny

Rendered fromshiny.Rnwusingutils::Sweaveon Jul 04 2024.

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

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

Package: ReportingTools 2.45.0

ReportingTools: Tools for making reports in various formats

Reporting on microarray differential expression

Reporting on RNA-seq differential expression

ReportingTools basics

ReportingTools shiny

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)