RGG: A general GUI Framework for R scripts

Visne, Ilhami; Dilaveroglu, Erkan; Vierlinger, Klemens; Lauss, Martin; Yıldız, Ahmet; Weinhäusel, Andreas; Noehammer, Christa; Leisch, Friedrich; Kriegner, Albert

doi:10.1186/1471-2105-10-74

Cited by 10 publications

(17 citation statements)

References 16 publications

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“…The back-end program consists of series of servlets [15] that communicates with system resources and utilities. Several open source applications and technologies [16-19] have been employed to enhance the flexibility and extendibility of this component. Open source R statistical analysis packages [18,19] are mainly in charge of the data analysis and processing.…”

Section: Methodsmentioning

confidence: 99%

SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies

Pirooznia¹,

Seifuddin²,

Goes³

et al. 2013

Source Code Biol Med

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BackgroundSurrogate variable analysis (SVA) is a powerful method to identify, estimate, and utilize the components of gene expression heterogeneity due to unknown and/or unmeasured technical, genetic, environmental, or demographic factors. These sources of heterogeneity are common in gene expression studies, and failing to incorporate them into the analysis can obscure results. Using SVA increases the biological accuracy and reproducibility of gene expression studies by identifying these sources of heterogeneity and correctly accounting for them in the analysis.ResultsHere we have developed a web application called SVAw (Surrogate variable analysis Web app) that provides a user friendly interface for SVA analyses of genome-wide expression studies. The software has been developed based on open source bioconductor SVA package. In our software, we have extended the SVA program functionality in three aspects: (i) the SVAw performs a fully automated and user friendly analysis workflow; (ii) It calculates probe/gene Statistics for both pre and post SVA analysis and provides a table of results for the regression of gene expression on the primary variable of interest before and after correcting for surrogate variables; and (iii) it generates a comprehensive report file, including graphical comparison of the outcome for the user.ConclusionsSVAw is a web server freely accessible solution for the surrogate variant analysis of high-throughput datasets and facilitates removing all unwanted and unknown sources of variation. It is freely available for use at http://psychiatry.igm.jhmi.edu/sva. The executable packages for both web and standalone application and the instruction for installation can be downloaded from our web site.

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Section: Methodsmentioning

confidence: 99%

SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies

Pirooznia¹,

Seifuddin²,

Goes³

et al. 2013

Source Code Biol Med

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“…Rgg is used to automatically create a Java GUI for the script parameters. 25 For subpopulation gating of flow cytometric and imagederived multivariate data, we used FaceJava, an implementation of the ISAC gating-ML standard that we use to store the gate definitions. JPEG2000 libraries from Aware, Inc. …”

Section: Software Componentsmentioning

confidence: 99%

Phaedra, a Protocol-Driven System for Analysis and Validation of High-Content Imaging and Flow Cytometry

2012

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High-content screening has brought new dimensions to cellular assays by generating rich data sets that characterize cell populations in great detail and detect subtle phenotypes. To derive relevant, reliable conclusions from these complex data, it is crucial to have informatics tools supporting quality control, data reduction, and data mining. These tools must reconcile the complexity of advanced analysis methods with the user-friendliness demanded by the user community. After review of existing applications, we realized the possibility of adding innovative new analysis options. Phaedra was developed to support workflows for drug screening and target discovery, interact with several laboratory information management systems, and process data generated by a range of techniques including high-content imaging, multicolor flow cytometry, and traditional high-throughput screening assays. The application is modular and flexible, with an interface that can be tuned to specific user roles. It offers user-friendly data visualization and reduction tools for HCS but also integrates Matlab for custom image analysis and the Konstanz Information Miner (KNIME) framework for data mining. Phaedra features efficient JPEG2000 compression and full drill-down functionality from dose-response curves down to individual cells, with exclusion and annotation options, cell classification, statistical quality controls, and reporting.

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“…3.0 (2001) to R 2.7.0 (2008) (Fox 2008;Ligges 2003;Visne et al 2009). RKWard utilizes functionality from a growing number of these packages, but avoids making the installation of all supported packages a pre-requirement to using RKWard at all.…”

Section: Package Managementmentioning

confidence: 99%

“…The number of R packages available from the Comprehensive R Archive Network (CRAN), Omegahat (http://www.omegahat.org/) and Bioconductor ) has grown exponentially since R 1.3.0 (2001) to R 2.7.0 (2008) (Fox 2008;Ligges 2003;Visne et al 2009). RKWard utilizes functionality from a growing number of these packages, but avoids making the installation of all supported packages a pre-requirement to using RKWard at all.…”

Section: Package Managementmentioning

confidence: 99%

“…XML is not only well suited to describe the layout of the GUI of plugins, but simple functional logic can also be represented (see also Visne et al 2009). ECMAScript was chosen for the generation of R commands within plugins, in particular due to its availability as an embedded scripting engine inside the Qt libraries.…”

Section: Choice Of Toolkit and Implementation Languagesmentioning

confidence: 99%

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RKWard: A Comprehensive Graphical User Interface and Integrated Development Environment for Statistical Analysis withR

Rödiger¹,

Friedrichsmeier²,

Kapat³

et al. 2012

J. Stat. Soft.

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R is a free open-source implementation of the S statistical computing language and programming environment. The current status of R is a command line driven interface with no advanced cross-platform graphical user interface (GUI), but it includes tools for building such. Over the past years, proprietary and non-proprietary GUI solutions have emerged, based on internal or external tool kits, with different scopes and technological concepts. For example, Rgui.exe and Rgui.app have become the de facto GUI on the Microsoft Windows and Mac OS X platforms, respectively, for most users. In this paper we discuss RKWard which aims to be both a comprehensive GUI and an integrated development environment for R. RKWard is based on the KDE software libraries. Statistical procedures and plots are implemented using an extendable plugin architecture based on ECMAScript (JavaScript), R, and XML. RKWard provides an excellent tool to manage different types of data objects; even allowing for seamless editing of certain types. The objective of RKWard is to provide a portable and extensible R interface for both basic and advanced statistical and graphical analysis, while not compromising on flexibility and modularity of the R programming environment itself.Keywords: GUI, integrated development environment, plugin, R. Background and motivationIn mid 1993 Ihaka and Gentleman published initial efforts on the computing language and programming environment R on the s-news mailing list. Ambitions for this project were to 2 RKWard: A Comprehensive GUI and IDE for R develop an S-like language without inheriting memory and performance issues. The source code of R was finally released in 1995, and since 1997 development has evolved under the umbrella of the R Development Core Team (R Development Core Team 2001, 2012aIhaka 1998). R does not include an advanced cross-platform graphical user interface (GUI) as known from other statistical software packages. However, R includes tools for building GUIs mainly based on Tcl/Tk (Dalgaard 2001(Dalgaard , 2002. Meanwhile a plethora of R GUIs have emerged (see Grosjean 2010, for a comprehensive list). In 2005 John Fox released version 1.0 of R Commander (Fox 2005, package Rcmdr), which can be considered a milestone in R GUI development; it was the first GUI implementation that was able to make statistical tests, plots and data manipulation easily accessible for R novices. John Fox stated that Rcmdr's target was to provide functionality for basic-statistical courses, though the features have increased over time beyond this (Fox 2005(Fox , 2007. In November 2002 Thomas Friedrichsmeier started the RKWard open-source software project with the goal to create a GUI for R based on KDE (KDE e.V. 2012) and Qt (Nokia Corporation 2012) technologies 1 .The scope of RKWard is deliberately broad, targeting both R novices and experts. For the first group, the aim is to allow any person with knowledge on statistical procedures to start using RKWard for their everyday work without having to learn anything about t...

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RGG: A general GUI Framework for R scripts

Abstract: Background: R is the leading open source statistics software with a vast number of biostatistical and bioinformatical analysis packages. To exploit the advantages of R, extensive scripting/ programming skills are required.

Cited by 10 publications

References 16 publications

SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies

SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies

Phaedra, a Protocol-Driven System for Analysis and Validation of High-Content Imaging and Flow Cytometry

RKWard: A Comprehensive Graphical User Interface and Integrated Development Environment for Statistical Analysis withR

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