RReportGenerator, Main
Aim
The aim of developing RReportGenerator consists in providing a simple and user-friendly graphical
user interface (GUI) allowing to run routine statistical analysis using the
R (R-project)
via predefined analysis scenarios in a local and independent manner. Of course, the large variety of
additional libraries on
CRAN
and
Bioconductor
may be used with the analysis scenarios.
The results (text, figures and tables) are automatically assembled into a report in pdf- (or dvi) format.
This may be accompanied by an additional file for exporting (specific) results to other applications
(spread-sheet programs, web-browser etc).
RReportGenerator can be used with a wide variety of applications.
Of course, some topics may be suited better for basic routine analysis than others.
At this time applications for treatment of high-throughput data in biological research, in particular, the following applications have been developed :
- Normalization and QC of microarrays,
- CGH-segmentation,
- Analysis of TCA-data (transfected cell array)
However, this system was not designed for replacing in depth analysis by a field-expert, who will be able to consider
optimally all special charcteristics/features of a particular data-set !
In overall, RReportGenerator represents an attempt to help people who are analyzing data by conveniently providing those elements
that can be generated by automatic procedures.
To make yourself an idea of what RReportGenerator can do (and what kind if results can be obtained),
please check out the Flash-Movie in the section 'Screenshots' .
News
RReportGenerator version 1.4.0 will be released soon
Windows : Please note that R 2.12.x won't work with RReportGenerator 1.3.x due to the different placement/organization of the executables !
The next version of RReportGenerator (1.4.0) will resolve this problem.
RReportGenerator has been featured in
Softpedia's database of (Windows) software programs. It was furthermore declared as 100% free of malware, spyware or viruses !
Reference
RReportGenerator is described in further detail in :
Raffelsberger W,
Krause Y, Mouliner L, Kieffer D, Morand AL, Brino L, Poch O;
RReportGenerator : Automatic reports from routine statistical analysis using R.
Bioinformatics 2008 Jan 15; 24(2): 276-278
This open access article is available through the journal 'Bioinformatics' (Oxford Journals).
Contact
wolfgang.raffelsberger (a t) igbmc.fr
Laboratoire de BioInformatique et Génomique Intégratives
(LBGI)
IGBMC, 67404 Illkirch Strasbourg, France
DOWNLOAD
Although REGISTRATION of RReportGenerator is not required we strongly encourage you to
subscribe HERE
for free.
Registered users may benefit of announcements of new versions and new scenarios.
Please choose the appropriate installer for RReportGenerator available under a GNU public license :
-
RReportGenerator (version 1.3.3)
for Windows®
-
RReportGenerator (version 1.3.3)
for Linux (x86) (e.g. Fedora, Ubuntu,.. )
-
A Mac version will be released soon.
The download contains an installer that includes the program, a
user-manual,
a basic set of
Analysis Scenarios
and some test-data.
Furthermore, RReportGenerator with source code has been made public on SourceFoge.net,
and the program is also available at Softpedia's database
of (Windows) software programs.
How to install RReportGenerator
General Note : While the installation of RReportGenerator is normally quite easy, the (potentially) tricky part consists in installing the pre-requisutes R and LaTeX/MiKTeX
installed properly, in particular for Windows-users who are not familier with using R and MiKTeX. Of course, this also concerns proper installation additional libraries
in R and LaTeX/MiKTeX. These libraries represent a main reason why using R and LaTeX/MiKTeX gets so powerful ! None of our analysis scenarios would work without some
non-default packages ... In this context we highly suggest to first install R and LaTeX/MiKTeX (see details below).
PRE-REQUISITES for running RReportGenerator :
Linux (x86 systems) :
The
statistics platform R and
LaTeX must be installed on your system.
Note that non-English installations of R-2.7.x or higher require RReportGenerator version 1.3.2 or higher !
Automatic installing missing libraries through R or LaTeX is in principle possible, but relies on several restrictions.
In general it is advisable to install all R and MiKTeX libraries needed (in the main installation path) before running RReportGenerator.
Check the analysis scenario "infos" button to see which libraries may be needed.
It is suggested to install all (addaitional) R-libraries in the same path as the main installation of R !
Further details for installing libraries are also given in the respective user-manuals and the help-pages
of
R and
LaTeX.
Windows systems :
The
statistics platform R (and all additional libraries used in the Analysis Scenarios you'll be using)
and
MiKTeX must be installed on your system.
Note : The most frequent difficulty for new users of RReportGenerator is the proper installation & configuration of MiKTeX !!
Non-English installations of R-2.7.x or higher require RReportGenerator version 1.3.2 or higher !
Automatically installing missing libraries through R or MiKTeX is in principle possible, but relies on several restrictions (see below).
In general, it is advisable to install MiKTeX libraries needed before running RReportGenerator.
You may use the RReportGenerator analysis scenario "infos" button to see the list of libraries that may be needed.
Further details for installing libraries are also given in the respective user-manuals and the help-pages
of
R and
MiKTeX.
Windows-VISTA and Windows-7 : Please note that additional/new packages should be located in the
same path as your installation of R !
Typically for installing new packages under Windows Vista it is necessary to launch R with a right click
as administrator (!),
in order to be able to access the main installation path (usually under "Program Files"..) !
Hint for MiKTeX libraries: The basic installation of MiKTeX doesn't contain all
libraries used with RReportGenerator scenarios (eg 'fancyvrb'). While installing MiKTeX you might
want to choose the option of letting MiKTeX directly install missing libraries
without asking.
Then, missing libraries may get installed 'on the fly' if needed (as long as the MiKTeX mirror responds at normal speed).
However, this will only work once you have properly configured/chosen a remote server for MiXTeX.
(So, if this is a fresh installation and you're missing 'fancyvrb', click on 'Miktex' / 'BrowePackages', and either select & install directly 'fancyvrb'
or click on 'Repository' and then 'Change Package Repository' to define internet settings and remote miroors.
Please make sure that you have sufficient rights for installing libraries ! )
If you choose the option of having MiKTeX ask you specifically before installing new libraries,
this won't work in the context of RReportGenerator (requires using the MiKTeX GUI) and
missing libraries won't get installed and in consequence no report files will be generated.
If you don't succed in getting missing libraries installed on the fly, you might try to
a) open MiKTeX via the 'Browse Packages' symbol and manually select the packages to be installed/updated via a MiKTeX
mirror of your choice.
b) Alternatively you could simply install MiKTeX with all its libraries (note that this takes much more
time for downloading and will occupy more disk-space).
Then you are ready to Download and INSTALL RReportGenerator !
INSTALLING RReportGenerator :
Please uninstall previous version(s) of RReportGenerator if you want to keep the installation in the same path as before.
Follow the instructions given by the installer (as default installation).
If you have multiple installations of R (or MiKTeX) on your system, you can choose which one should be used via's RReportGenerator
configuration window :
Click on Help/Configure : If you opt to manually change/choose the installation path (via Help/Configure) please always select the directory
one level underneith the directory "/bin". For example, in the case of a default installation
on Windows this might be something like
'C:\Program Files\MiKTeX 2.7\miktex' or
'C:\Program Files\R\R-2.7.0'
(which is in both cases the path containing a directory called
bin hodling the main exectuable).
Please use recent versions of R, MikTex and/or LaTeX. Although RReportGenerator itself basically supports most older versions of R,
most of the Analysis Scenarios require recent versions of these programs and their associated packages. Besides, it is very important that the versions of
the additional packages and libraries match exacetly the version of the corresponding programs (e.g. libraries for MikTex 2.6 won't work with MetkTex 2.5).
For installing additional Bioconductor packages from within R, please look at the instructions
on
www.bioconductor.org/download .
The configuration file of RReportGenerator is saved in the
.RRG directory (which is normally located in something
like
C:\Documents and Settings\yourAcount\Application Data\ (Windows, this path may be 'hidden'), or with Lunix in your home-directory )
before launching RReportGenerator the first time. Note that re-installing RReportGenerator doesn't affect the configuration (since it's RReportGenerator itself
and not the installer, who's creating & managing the configuration), for en entire fresh start you may have to manually delete this file.
For users upgrading form RReportGenerator 1.2 it is suggested to remove the old configuration file in the
.RRG directory.
Using RReportGenerator
For details about using RReportGenerator please look at the
user-manual.
The overall concept of using RReportGenerator consists in the following steps :
a) Identify an analysis scenario fitting your needs of data-treatment and select corresponding "Analysis Scenario File"
(the "Library-button" permits to access all analysis scenarios available on our web-server and the "Infos" allows displaying a brief resume about the various scenarios).
b) Select your data to be treated by the analysis scenario.
c) Choose a name for the resulting analysis report and the folder where it should be saved.
(optinal:) Check if you would like any of the optinal items or settings
d) Launch "Generate Report"
In general we suggest our users to use preferentially those analysis scenarios accesible through the button 'Library' for loading
analysis sceanrios, since these sceanrios are frequently updated and typically provide more stability as well as features/functionality.
Registered users are welcome to contact us
with ideas for improving & extending existing analysis scenarios or to suggest new applications where novel analysis
scenarios may help your work. Registration
is free of charge.
Flash moovie showing the use of RReportGenerator
for running automatic QC of Affymetrix gene expression data.
Changes
27 Jun 2007 : RReportGenenerator Version 1.2 (for Windows) has been released together with basic set of analysis scenarios
5 Sept 2007 : RReportGenenerator Version 1.3 has been released !
This version has been compiled for Linux and for Windows.
A new function allowing to retreive Analysis Scenarios directly from the web has been added.
18 Oct 2007 : Analysis Scenarios for CGH data were improved.
23 Oct 2007 : Analysis Scenario for printed micorarrays analyzed using MAIA data was improved.
23 Oct 2007 : Analysis Scenario AffyQC2 for Affymetrix micorarray QC was improved.
30 Oct 2007 : RReportGenenerator Version 1.3.1 with improved support for Windows Vista has been released.
31 Oct 2007 : This web-site has been redesigned.
13 Nov 2007 : New personalization options for Scenarios "summarizeTCA_fromExcel" (Version: 1.2.10) in Excel files via the 'Plate Setup' sheet were added (+ minor bugfixes)
14 Nov 2007 : Scenario AffyQC2 (Version 1.0.9) for Affymetrix micorarray QC was made more robust to avoid problems with custom arrays or with 'exotic' species.
29 Nov 2007 : Scenario combineMAIAdata1.rnw Version 1.1.4 has been released (minor bugfixes for small number of arrays, improved layout).
04 Dec 2007 : Scenario combineMAIAdata1.rnw Version 1.1.6 has been released : new warnings, improved support for unusual file-names.
05 Dec 2007 : Installation information in "How to use" on this web-page was updated
06 Dec 2007 : Scenario automAffyQC1.Rnw Version 1.1.0 has been released : improved support for up to 300 microarrays.
14 Jan 2008 : All references in scenarions were updated with full reference of the publication of RReportGenerator.
14 Jan 2008 : Scenario automAffyQC1.Rnw Version 1.1.1 has been released : Principal component analysis and plot of all arrays were added.
25 & 30 Jan 2008 : Minor changes to text in 'Main'.
11 Mar 2008 : Scenario automAffyQC1.Rnw version 1.2.0 has been released : faster and resulting pdf files are up to 50% smaller (better handeling of resolution for graphics).
11 Mar 2008 : Scenario automAffyQC2.Rnw version 1.2.0 : like automAffyQC1.Rnw but uses gcrma and plots additional hierarchical clustering with bootstrap pvalues; up to 50% smaller resulting pdf files (better handeling of resolution in graphics).
11 Mar 2008 : Scenario summarizeTCA_fromExcel.Rnw version 1.2.16 : allows handeling of data with just a single type of measure of cells, supports up to 10 sheets of input-data, new options for setting threshold based on controls.
6 Mai 2008 : A problem with non-English installations of R-2.7.0 has been noted (this concerns RReportGenerator versions 1.2, 1.3.0 and 1.3.1).
15 Mai 2008 : RReportGenerator version 1.3.2 has been released ! (This version gives full compatibility to R-2.7.x installations independent of language settings)
6 June 2008 : Minor changes to installation instructions.
30 June 2008 : The tab 'Installation' was reedited on website.
14 Aug 2008 : RReportGenerator version 1.3.3 has been released ! (This version allows preferred paper formt setting and (Windows:) customizing the memory allocated to R)
18 Aug 2008 : Correction of typos on our website.
18 Aug 2008 : Scenario automAffyQC1.Rnw version 1.2.1 has been released : additional version documentation of all Bioconductor packages used, additional boxplot of normalized data.
18 Dec 2008 : Scenario summarizeTCA_fromExcel.Rnw, version 1.2.17 has been released : More robustness for missing data (handeling of NA), minor bug-fixes.
02 Jan 2009 : Scenario summarizeTCA_fromExcel.Rnw, version 1.2.19 : Summary of replicate samples in exported data, minor graphical improvements & bug-fixes.
13 Jan 2009 : RReportGenerator project with source code for most recent stable version (RReportGenerator 1.3.3) has been made public on SourceFoge.net
04 Feb 2009 : Scenario summarizeTCA_fromExcel.Rnw, version 1.2.20 : Minor graphical improvements display of file-names and Boxplots.
17 Apr 2009 : Scenario segmentCGH3.Rnw, version 1.1.1 for CGH segmentation: Now the sample is supposed to be in Cy5 and reference in Cy3; improved R-library version documentation.
25 Dec 2009 : RReportGenerator has been featured in
Softpedia's database of (Windows) software programs. It was furthermore declared as 100% free of malware, spyware or viruses.
26 Feb 2010 : Scenario automAffyQC2.Rnw version 1.2.2 : better short names of arrays and fixed compatibility with Bioconductor v2.5
03 Mar 2010 : Scenario automAffyQC2.Rnw version 1.2.3 : minor bug-fix in short names of arrays
08 Mar 2010 : Scenario automAffyQC2.Rnw version 1.2.5 : adjusted to handle projects with just 2 arrays, minor bug-fix in short names of arrays
12 Aug 2010 : Scenario automAffyQC1.Rnw version 1.2.5 : automatic installing of missing libraries, minor bug-fix in short names of arrays
12 Aug 2010 : Scenario automAffyQC2.Rnw version 1.2.7 : automatic installing of missing libraries, minor bug-fix in short names of arrays
14 Jan 2011 : Scenario automAffyQC2.Rnw version 1.2.8 : automatically detects if file or folder was given (preparation for RReportGenerator 1.3.4)
This project was also presented at the
UseR! 2008
conference in Dortmund, Germany : The
slides of our presentation are available.
The publication of RReportGenerator has been cited in:
- Thiersch et al, BMC Genomics 2008 : Analysis of the retinal gene expression profile after hypoxic preconditioning.
- Kalathur et al, BMC Genomics 2008 : RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina.
- Barton et al, BMC Bioinformatics 2008 : EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management.
- Reichman et al, Hum Mol Genet 2010 : The homeobox gene CHX10/VSX2 regulates RdCVF promoter activity in the inner retina.
- Leprêtre et al, NAR 2010 : Waved aCGH: to smooth or not to smooth.
- Cronin et al, Cell Death Differ. 2010 : The disruption of the rod-derived cone viability gene leads to photoreceptor dysfunction and susceptibility to oxidative stress.
- Berge et al, J Comput Biol. 2010 : Multidimensional Fitting for Multivariate Data Analysis.
- Ochs et al, Springer US, 10.1007/978-1-4419-5714-6_6 Genomics Data Analysis Pipelines, in: Biomedical Informatics for Cancer Research.
- Wunderlich et al, Invest Ophthalmol Vis Sci. 2010 : Metallothioneins I=II and their receptor megalin are altered in inherited photorecpetor degeneration.
Disclaimer
RReportGenerator is free software (under the Free Software Foundation
GNU General Public License
) WITHOUT ANY WARRANTY.
The authors take NO responsibility for any malfunctioning of this program, other components,
the correctness or interpretation of results.
Please note that RReportGenerator was NOT designed to replace in depth analysis by a specialist in the field, who should be able
to consider properly all special features of a particular data-set.
RReportGenerator represents rather an attempt to help the people in the field by easily and quickly providing those elements that can be generated through automatic procedures.
