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Nozzle R Package

Nozzle is an R package for generation of reports in high-throughput data analysis pipelines. Nozzle reports are implemented in HTML, JavaScript, and Cascading Style Sheets (CSS), but developers do not need any knowledge of these technologies to work with Nozzle. Instead they can use a simple R API to design and implement powerful reports with advanced features such as foldable sections, zoomable figures, sortable tables, and supplementary information. Please cite our Bioinformatics paper if you are using Nozzle in your work.

Documentation

Presentations

Report Examples

Code Examples

Download and Installation

Nozzle is available on CRAN and can be installed directly from the R shell.

Archived Versions

For reference only. As of version 1.0-0 Nozzle should be obtained from CRAN. Please note that the releases before 1.0-0 do not contain any documentation within the R package.

Name Size Creator Creation Date Comment  
ZIP Archive Nozzle.R1_1.1-1.tar.gz 92 kB Nils Gehlenborg May 15, 2013 11:46 Latest Release. Also available from CRAN: http://cran.r-project.org/package=Nozzle.R1  
ZIP Archive Nozzle.R1_1.1-0.tar.gz 92 kB Nils Gehlenborg May 14, 2013 14:05    
ZIP Archive Nozzle.R1_1.0-0.tar.gz 89 kB Nils Gehlenborg Jan 08, 2013 06:49    
ZIP Archive Nozzle.R1_0.3-1.tar.gz 78 kB Nils Gehlenborg Sep 06, 2012 16:10    
ZIP Archive Nozzle.R1_0.3-0.tar.gz 77 kB Nils Gehlenborg Feb 17, 2012 10:04    
ZIP Archive Nozzle.R1_0.2-99.tar.gz 69 kB Nils Gehlenborg Aug 04, 2011 13:43 Preview Release (do not use in Firehose)  
ZIP Archive Nozzle.R1_0.2-1.tar.gz 49 kB Nils Gehlenborg Aug 04, 2011 13:37    
ZIP Archive Nozzle.R1_0.2-2.tar.gz 49 kB Nils Gehlenborg Aug 04, 2011 13:37    
ZIP Archive Nozzle.R1_0.2-3.tar.gz 57 kB Nils Gehlenborg Aug 04, 2011 13:37    
ZIP Archive Nozzle.R1_0.1-0.tar.gz 15 kB Nils Gehlenborg Aug 04, 2011 13:37    
ZIP Archive Nozzle.R1_0.2-0.tar.gz 49 kB Nils Gehlenborg Aug 04, 2011 13:37    

GitHub Repository

The GitHub repository for Nozzle is at http://github.com/parklab/nozzle.

License

Nozzle is open source software and licensed under the LGPL version 2.1.

Contact

All questions related to Nozzle should be sent directly to Nils Gehlenborg (nils@hms.harvard.edu). Questions about Nozzle related to the Firehose Analysis pipeline should be directed to gdac@broadinstitute.org.

Nozzle & Firehose

Nozzle Reports for Monthly TCGA Firehose Analysis Runs

  • Dashboard (public reports available starting January 2012)

Guidelines for Firehose Developers

Technical Notes on Integrating Nozzle into Firehose Modules

  • The path to nozzle libraries can be passed into your R script using the special variable in your manifest/hydrant.deploy file: <nozzle.path> (evaluates to /xchip/tcga/Tools/Nozzle/v1.current). In other words, Firehose will take care of providing this value without the need to expose it to the task configuration (just like <libdir>).
  • To load the libraries in R: require("Nozzle.R1", lib.loc=nozzlePath, quietly=TRUE); Where nozzlePath is a variable passed into the R script containing <nozzle.path>.
  • All the resources referenced in your report must be in the top directory. For example, nesting of directories for figure image files will not display correctly in the Firehose UI.
  • The report must be named nozzle.html. This is the default file name produced by writeReport(myReport). However, writeReport(myReport, filename="report.html") will not work. 
  • In some cases, use of the <R> variable in the manifest/hydrant.deploy file has caused problems. When to use <R> and when to use a direct path to Rscript is currently unclear.