ReportingTools

This is the development version of ReportingTools; for the stable release version, see ReportingTools.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11

Tools for making reports in various formats

Bioconductor version: Development (3.24)

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>

Citation (from within R, enter citation("ReportingTools")):

Jason A. Hackney, Melanie Huntley, Jessica L. Larson, Christina Chaivorapol, Gabriel Becker, and Josh Kaminker. ReportingTools: Tools for making reports in various formats. doi:10.18129/B9.bioc.ReportingTools, R package version 2.53.0, https://bioconductor.org/packages/ReportingTools.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataRepresentation, GO, GeneSetEnrichment, ImmunoOncology, Microarray, RNASeq, Software, Visualization
Version	2.53.0
In Bioconductor since	BioC 2.11 (R-2.15) (14 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
System Requirements
URL

Suggests	RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla, org.Sc.sgd.db, rmarkdown, markdown
Linking To
Enhances
Depends On Me
Imports Me	affycoretools
Suggests Me	cpvSNP, EnrichmentBrowser, GSEABase, npGSEA
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	ReportingTools_2.53.0.tar.gz
Windows Binary (x86_64)	ReportingTools_2.53.0.zip
macOS Binary (big-sur-x86_64)	ReportingTools_2.53.0.tgz
macOS Binary (sonoma-arm64)	ReportingTools_2.53.0.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