[Bioc-devel] New version of PROSTAR and DAPAR packages

[Samuel Wieczorek]

Dear Bioconductor developers, As the Bioconductor was released, I would 
like to present the evolution of the packages DAPAR and Prostar and the 
introduction of the package DAPARdata. *DAPAR*and*ProStaR*form a 
software suite for quantitative analysis of mass spectrometry based 
proteomics, more specifically designed to process relative quantitative 
data from discovery experiments. It is composed of two distinct R packages :

  * Prostar
    <http://www.bioconductor.org/packages/release/bioc/html/Prostar.html>package:
    the web based Graphical User Interface to DAPAR (based on Shiny)
  * DAPAR
    <http://www.bioconductor.org/packages/release/bioc/html/DAPAR.html>
    a collection of tools and graphs dedicated to proteomic analysis
  * DAPARdata: an experiment package that contains two datasets which
    are respectivey protein and peptide quantitative data. 

In this new release, several major features have been introduced:

  * The interface of Prostar is now based on "Navbar menus "which allow
    more space for the plots and data tables in the screen and is easier
    to use
  * An aggregation tool has been implemented which aggregates peptides
    into proteins
  * In the differential analysis tool, calibration plots have been
    integrated from the package cp4p in order to help the user to choose
    the correct p-value threshold w.r.t the FDR. 

Finally, a tutorial is available and is the perfect companion of 
Prostar's user manual

The development of these two packages is very active and we work now on 
new functionalities and processing tools that will be available soon Do 
not hesitate to test this tool and to give me a feedback of your 
experience. Best regards
Samuel Wieczorek

-- Samuel Wieczorek Etude de la Dynamique des Proteomes (EDyP) 
http://edyp.fr/ Laboratoire Biologie a Grande Echelle (BGE) U1038 
INSERM/CEA/UJF Institut de Recherches en Technologies et Sciences pour 
le Vivant (iRTSV) CEA/Grenoble 17 rue des Martyrs F-38054 Grenoble Cedex 
9 Tel : 04 38 78 44 14 Tel : 04 38 78 34 40 [[alternative HTML version 
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-- *Samuel Wieczorek Etude de la Dynamique des Protéomes (EDyP)* 
*Laboratoire Biologie à Grande Echelle (BGE)* *U1038 INSERM / CEA / UGA* 
*Biosciences and Biotechnology Institute of Grenoble (BIG)* *CEA / 
Grenoble* *17 avenue des Martyrs* *F-38054 Grenoble Cedex 9* */Tél. : 
04.38.78.44.14/**/Fax : 04.38.78.50.51/*

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