Difference between revisions of "RReportGenerator English"
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| − | [http://alnitak.u-strasbg.fr/~wraff/RReportGenerator/index.html RReportGenerator] provides a 'report-generator' tool for routine automatic statistical analysis in a highly user-friendly way via a graphical user inferface (GUI). <br> | + | [http://alnitak.u-strasbg.fr/~wraff/RReportGenerator/index.html RReportGenerator] provides a 'report-generator' tool for routine automatic statistical analysis with "R" in a highly user-friendly way via a graphical user inferface (GUI). <br> |
| − | While the statistical platform "[[R]]", [http://www.r-project.org/ see also the official site of R] and the vast collection of additional modules on [http://www.r-project.org/ CRAN] and [http://www.bioconductor.org Bioconductor] allow very powerful statistical analysis, it’s particular command-line syntax renders the program | + | While the statistical platform "[[R]]", [http://www.r-project.org/ see also the official site of R], and the vast collection of additional modules on [http://www.r-project.org/ CRAN] and [http://www.bioconductor.org Bioconductor] allow very powerful statistical analysis, it’s particular command-line syntax renders the program difficult to access for non-statisticians. In this context we have developed a program designed for routine executing of a predefined "analysis scenarios" for a given problem which can be easily operated by non-experienced users via it’s graphical interface. In turn a pdf-report with the analysis results, tables and figures is generated that can be accompanied by supplemental data-sets for export to other programs (e.g. Excel). |
Analysis scenarios are written in the [http://www.r-project.org/ R] and [http://www.latex-project.org/ Latex] language and allow following a path of multiple steps of data-treatment including flexible generation of graphs and potential identification of warnings. The graphical user interface of [http://alnitak.u-strasbg.fr/~wraff/RReportGenerator/index.html RReportGenerator] allows the user to simply choose among predefined analysis-scenarios to be applied this to a given data-set. In turn a pdf-report with the analysis results, tables and figures is generated that can be accompanied by supplemental data-sets for export to other programs (e.g. Excel). An example of mouse retina transcription profiling illustrates suitable tasks of quality control and analysis for automated analysis. | Analysis scenarios are written in the [http://www.r-project.org/ R] and [http://www.latex-project.org/ Latex] language and allow following a path of multiple steps of data-treatment including flexible generation of graphs and potential identification of warnings. The graphical user interface of [http://alnitak.u-strasbg.fr/~wraff/RReportGenerator/index.html RReportGenerator] allows the user to simply choose among predefined analysis-scenarios to be applied this to a given data-set. In turn a pdf-report with the analysis results, tables and figures is generated that can be accompanied by supplemental data-sets for export to other programs (e.g. Excel). An example of mouse retina transcription profiling illustrates suitable tasks of quality control and analysis for automated analysis. | ||
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Predefined analysis-scenarios for automatic analysis have been developed for the following areas : | Predefined analysis-scenarios for automatic analysis have been developed for the following areas : | ||
| − | # Transcriptomics : Analysis scenarios | + | # Transcriptomics : Analysis scenarios combining a large collection of different types of quality control (QC) for [http://www.affymetrix.com Affymetrix] genes expression chips . <br>There is also a scenario for QC of printed arrays (images analyzed by [http://bioinfo.curie.fr/projects/maia/ MAIA]). |
| − | # Comparative genomic hybridization [http://en.wikipedia.org/wiki/Comparative_genomic_hybridization CGH]: <br> The available scenarios use 3 or 4 different algorithms of segmentation and allow supperposing the results. | + | # Comparative genomic hybridization, [http://en.wikipedia.org/wiki/Comparative_genomic_hybridization CGH]: <br> The available scenarios use 3 or 4 different algorithms of segmentation and allow supperposing the results. |
# Transfected cell array (TCA) : The analysis scenario(s) may be used to define a threshold based on non-treated control samples and to report a summary about all samples tested on a transfection plate. | # Transfected cell array (TCA) : The analysis scenario(s) may be used to define a threshold based on non-treated control samples and to report a summary about all samples tested on a transfection plate. | ||
| − | Please check the information available with the analysis scenarios available through the www-library in RReportGenerator for further details. | + | Please check the supplemental information available with the analysis scenarios available through the www-library in RReportGenerator for further details. Using the www-library directly accesses the most recent versions of our public analysis scenarios. |
| − | In conclusion, [http://www-bio3d-igbmc.u-strasbg.fr/~wraff/RReportGenerator/index.html RReportGenerator] allows to run routine statistical analysis while benefitting from the environement of R via a convenient graphical interface (GUI) allowing | + | In conclusion, [http://www-bio3d-igbmc.u-strasbg.fr/~wraff/RReportGenerator/index.html RReportGenerator] allows to run routine statistical analysis while benefitting from the environement of R via a convenient graphical interface (GUI) allowing inexperienced users to run routine analysis tasks. |
| − | Reference: <br>The program is published | + | Reference: <br>The program is published and accessible as open access : |
| − | Raffelsberger W, Krause Y, Mouliner L, Kieffer D, Morand AL, Brino L, Poch O; | + | Raffelsberger W, Krause Y, Mouliner L, Kieffer D, Morand AL, Brino L, Poch O; <br> |
| − | ReportGenerator : Automatic reports from routine statistical analysis using R. [http://bioinformatics.oxfordjournals.org/cgi/reprint/btm556v1 Bioinformatics | + | ReportGenerator : Automatic reports from routine statistical analysis using R. [http://bioinformatics.oxfordjournals.org/cgi/reprint/btm556v1 Bioinformatics 2008, 24(2), 276-278] |
<br>... voir cette page en Francais : [[RReportGenerator]] | <br>... voir cette page en Francais : [[RReportGenerator]] | ||
Revision as of 12:44, 21 January 2008
RReportGenerator provides a 'report-generator' tool for routine automatic statistical analysis with "R" in a highly user-friendly way via a graphical user inferface (GUI).
While the statistical platform "R", see also the official site of R, and the vast collection of additional modules on CRAN and Bioconductor allow very powerful statistical analysis, it’s particular command-line syntax renders the program difficult to access for non-statisticians. In this context we have developed a program designed for routine executing of a predefined "analysis scenarios" for a given problem which can be easily operated by non-experienced users via it’s graphical interface. In turn a pdf-report with the analysis results, tables and figures is generated that can be accompanied by supplemental data-sets for export to other programs (e.g. Excel).
Analysis scenarios are written in the R and Latex language and allow following a path of multiple steps of data-treatment including flexible generation of graphs and potential identification of warnings. The graphical user interface of RReportGenerator allows the user to simply choose among predefined analysis-scenarios to be applied this to a given data-set. In turn a pdf-report with the analysis results, tables and figures is generated that can be accompanied by supplemental data-sets for export to other programs (e.g. Excel). An example of mouse retina transcription profiling illustrates suitable tasks of quality control and analysis for automated analysis.
The program RReportGenerator (compiled for Windows and Linux) and further informations, tutorial and examples are available on Wolfgang's site
Applications :
Predefined analysis-scenarios for automatic analysis have been developed for the following areas :
- Transcriptomics : Analysis scenarios combining a large collection of different types of quality control (QC) for Affymetrix genes expression chips .
There is also a scenario for QC of printed arrays (images analyzed by MAIA). - Comparative genomic hybridization, CGH:
The available scenarios use 3 or 4 different algorithms of segmentation and allow supperposing the results. - Transfected cell array (TCA) : The analysis scenario(s) may be used to define a threshold based on non-treated control samples and to report a summary about all samples tested on a transfection plate.
Please check the supplemental information available with the analysis scenarios available through the www-library in RReportGenerator for further details. Using the www-library directly accesses the most recent versions of our public analysis scenarios.
In conclusion, RReportGenerator allows to run routine statistical analysis while benefitting from the environement of R via a convenient graphical interface (GUI) allowing inexperienced users to run routine analysis tasks.
Reference:
The program is published and accessible as open access :
Raffelsberger W, Krause Y, Mouliner L, Kieffer D, Morand AL, Brino L, Poch O;
ReportGenerator : Automatic reports from routine statistical analysis using R. Bioinformatics 2008, 24(2), 276-278
... voir cette page en Francais : RReportGenerator
