ReportingTools: an automated result processing and presentation toolkit for high-throughput genomic analyses.
It is common for computational analyses to generate large amounts of complex data that are difficult to process and share with collaborators. Standard methods are needed to transform such data into a more useful and intuitive format. We present ReportingTools, a Bioconductor package, that automatically recognizes and transforms the output of many common Bioconductor packages into rich, interactive, HTML-based reports. Reports are not generic, but have been individually designed to reflect content specific to the result type detected. Tabular output included in reports is sortable, filterable and searchable and contains context-relevant hyperlinks to external databases. Additionally, in-line graphics have been developed for specific analysis types and are embedded by default within table rows, providing a useful visual summary of underlying raw data. ReportingTools is highly flexible and reports can be easily customized for specific applications using the well-defined API.


BACKGROUND
The ReportingTools package is implemented in R and available from Bioconductor (version ≥ 2.11) at the URL: http://bioconductor.org/packages/release/bioc/html/ReportingTools.html. Installation instructions and usage documentation can also be found at the above URL.
Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA and Department of Statistics, University of California at Davis, Davis, CA 95616, USA.
Melanie A
MA
Huntley
Jessica L
JL
Larson
Christina
C
Chaivorapol
Gabriel
G
Becker
Michael
M
Lawrence
Jason A
JA
Hackney
Joshua S
JS
Kaminker
D000465:Algorithms; D019295:Computational Biology; D016208:Databases, Factual; D020869:Gene Expression Profiling / Q000379:methods*; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D012984:Software