ReportingTools

DOI: 10.18129/B9.bioc.ReportingTools    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ReportingTools.

Tools for making reports in various formats

Bioconductor version: 3.9

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

Maintainer: Jason A. Hackney <hackney.jason at gene.com>, Gabriel Becker <becker.gabe at gene.com>, Jessica L. Larson <larson.jessica at gmail.com>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ReportingTools")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ReportingTools")

 

HTML	R Script	Knitr and ReportingTools
PDF	R Script	Reporting on microarray differential expression
PDF	R Script	Reporting on RNA-seq differential expression
PDF	R Script	ReportingTools basics
PDF	R Script	ReportingTools shiny
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataRepresentation, GO, GeneSetEnrichment, ImmunoOncology, Microarray, RNASeq, Software, Visualization
Version	2.24.0
In Bioconductor since	BioC 2.11 (R-2.15) (7 years)
License	Artistic-2.0
Depends	methods, knitr, utils
Imports	Biobase, hwriter, Category, GOstats, limma(>= 3.17.5), lattice, AnnotationDbi, edgeR, annotate, PFAM.db, GSEABase, BiocGenerics(>= 0.1.6), grid, XML, R.utils, DESeq2(>= 1.3.41), ggplot2, ggbio, IRanges
LinkingTo
Suggests	RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla, org.Sc.sgd.db
SystemRequirements
Enhances
URL
Depends On Me	rnaseqGene
Imports Me	affycoretools, EnrichmentBrowser
Suggests Me	cpvSNP, GSEABase, npGSEA
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ReportingTools_2.24.0.tar.gz
Windows Binary	ReportingTools_2.24.0.zip
Mac OS X 10.11 (El Capitan)	ReportingTools_2.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ReportingTools
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ReportingTools
Package Short Url	https://bioconductor.org/packages/ReportingTools/
Package Downloads Report	Download Stats