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> |
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 very 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). | 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 very 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. | |
The program [http://http://alnitak.u-strasbg.fr/~wraff/RReportGenerator/index.html RReportGenerator] (compiled for Windows and Linux) and further informations, tutorial and examples are available [http://www-bio3d-igbmc.u-strasbg.fr/~wraff on Wolfgang's site] | The program [http://http://alnitak.u-strasbg.fr/~wraff/RReportGenerator/index.html RReportGenerator] (compiled for Windows and Linux) and further informations, tutorial and examples are available [http://www-bio3d-igbmc.u-strasbg.fr/~wraff on Wolfgang's site] | ||
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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 resuming 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] | + | # 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. | ||
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 inexpereienced users to run routine analysis tasks. | 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 inexpereienced users to run routine analysis tasks. | ||
| − | Reference: <br>The program is published in : Raffelsberger W, Krause Y, Mouliner L, Kieffer D, Morand AL, Brino L, Poch O; | + | Reference: <br>The program is published in : |
| − | ReportGenerator : Automatic reports from routine statistical analysis using R. Bioinformatics 2007, in press | + | Raffelsberger W, Krause Y, Mouliner L, Kieffer D, Morand AL, Brino L, Poch O; |
| + | ReportGenerator : Automatic reports from routine statistical analysis using R. [http://bioinformatics.oxfordjournals.org/cgi/reprint/btm556v1 Bioinformatics 2007, in press] | ||
<br>... voir cette page en Francais : [[RReportGenerator]] | <br>... voir cette page en Francais : [[RReportGenerator]] | ||
Revision as of 15:32, 29 November 2007
RReportGenerator provides a 'report-generator' tool for routine automatic statistical analysis 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 very 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 resuming 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 information available with the analysis scenarios available through the www-library in RReportGenerator for further details.
In conclusion, RReportGenerator allows to run routine statistical analysis while benefitting from the environement of R via a convenient graphical interface (GUI) allowing inexpereienced users to run routine analysis tasks.
Reference:
The program is published in :
Raffelsberger W, Krause Y, Mouliner L, Kieffer D, Morand AL, Brino L, Poch O;
ReportGenerator : Automatic reports from routine statistical analysis using R. Bioinformatics 2007, in press
... voir cette page en Francais : RReportGenerator
