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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ReportingTools")
In most cases, you don't need to download the package archive at all.
ReportingTools
Tools for making reports in various formats
Bioconductor version: 2.14
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 gene.com>
Citation (from within R,
enter citation("ReportingTools")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ReportingTools")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ReportingTools")
| R Script | Reporting on microarray differential expression | |
| R Script | Reporting on RNA-seq differential expression | |
| R Script | ReportingTools basics | |
| R Script | ReportingTools shiny | |
| HTML | R Script | Knitr and ReportingTools |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Bioinformatics, DataRepresentation, Enrichment, GO, GeneSetEnrichment, Microarray, RNASeq, Software, Visualization |
| Version | 2.4.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) |
| License | Artistic-2.0 |
| Depends | methods, knitr |
| 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), IRanges, ggplot2, ggbio |
| Suggests | RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | affycoretools, biosvd |
| Suggests Me | GSEABase, npGSEA |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ReportingTools_2.4.0.tar.gz |
| Windows Binary | ReportingTools_2.4.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | ReportingTools_2.4.0.tgz |
| Mac OS X 10.9 (Mavericks) | ReportingTools_2.4.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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