output$References <- renderText({
txt<- "<strong><font size=\"5\">HELP</font></strong>
<br><hr color:\"blue\"><br>
<strong><font size=\"4\">User manual:</font></strong>
<a href=\"https://www.bioconductor.org/packages/release/bioc/vignettes/
Prostar/inst/doc/Prostar_UserManual.pdf\"
title=\"here\" target=\"_blank\">here</a>
<br><br>
<strong><font size=\"4\">Tutorial:</font></strong>
<a href=\"http://bioconductor.org/packages/release/bioc/vignettes/
Prostar/inst/doc/Prostar_Tutorial.pdf\"
title=\"here\" target=\"_blank\">here</a>
<br><br>
<strong><font size=\"4\">Contact:</font></strong><br>
If you need any help, but also if you wish to make comments
or suggestions, please contact Samuel Wieczorek, Florence Combes or
Thomas Burger (firstname.lastname@cea.fr)<br><br>
<strong><font size=\"4\">Additional ressources:</font></strong>
<ul>
<li> ProStaR reference manual:
<a href=\"https://www.bioconductor.org/packages/release/bioc/manuals/
Prostar/man/Prostar.pdf\"
title=\"here\" target=\"_blank\">here</a>
</li>
<li> DAPAR reference manual: <a href=\"https://www.bioconductor.org/
packages/release/bioc/manuals/DAPAR/man/DAPAR.pdf\"
title=\"here\" target=\"_blank\">here</a>
</li>
<li> MSnbase package: <a href=\"https://www.bioconductor.org/packages/
release/bioc/html/MSnbase.html\" title=\"here\" target=\"_blank\">here</a>
</li>
<li> Cp4p tutorial: <a href=\"https://cran.r-project.org/web/
packages/cp4p/cp4p.pdf\"
title=\"here\" target=\"_blank\">here</a>
</li>
</ul>
<br><br>
<strong><font size=\"4\">Our referenced works:</font></strong>
<ol>
<li> S. Wieczorek, F. Combes, C. Lazar, Q. Giai-Gianetto, L. Gatto,
A. Dorffer, A.-M. Hesse, Y. Coute, M. Ferro, C. Bruley, T. Burger.
DAPAR & ProStaR: software to perform statistical analyses in
quantitative discovery proteomics, <i>Bioinformatics</i>, 2016
</li>
<li> C. Lazar, L. Gatto, M. Ferro, C. Bruley, T. Burger. Accounting
for the multiple natures of missing values in label-free quantitative
proteomics datasets to compare imputation strategies. <i>Journal of
Proteome Research</i>, 15(4):1116-25, 2016.
</li>
<li> Q. Giai Gianetto, F. Combes, C. Ramus, C. Bruley, Y. Coute,
T. Burger. Calibration Plot for Proteomics (cp4p): A graphical tool
to visually check the assumptions underlying FDR control in
quantitative experiments. <i>Proteomics</i>, 16(1):29-32, 2016.
</li>
<li> Q. Giai Gianetto, Y. Coute, C. Bruley, T. Burger. Uses and
misuses of the fudge factor in quantitative discovery proteomics.
<i>Proteomics</i>, 16(14):1955-60, 2016.
</li>
<li> Q. Giai Gianetto, C. Lazar, S. Wieczorek, C. Bruley, Y. Coute and
T. Burger. Multiple imputation strategy for mass spectrometry-based
proteomic data (under preparation)
</li>
</ol>
<br><br>
<strong><font size=\"4\">Other references:</font></strong>
<ol start=6>
<li> Bolstad BM (2016). preprocessCore: A collection of pre-processing
functions. R package version 1.36.0,
<a href=\"https://github.com/bmbolstad/preprocessCore\"
title=\"here\" target=\"_blank\">
https://github.com/bmbolstad/preprocessCore</a>
<li> Hastie T, Tibshirani R, Narasimhan B and Chu G (2016).
impute: Imputation for microarray data. R package version 1.48.0
</li>
<li> Ported to R by Alvaro A. Novo. Original by Joseph L. Schafer
<jls@stat.psu.edu>. (2013). norm: Analysis of
multivariate normal datasets with missing values. R package
version 1.0-9.5.
<a href=\"https://CRAN.R-project.org/package=norm\"
title=\"norm on CRAN\" target=\"_blank\">norm on CRAN</a>
</li>
</ol>"
HTML(txt)
})
#-------------------------------------------------------------------
output$aboutText <- renderUI({
busyIndicator("Calculation in progress",wait = 0)
t <- sessionInfo()
daparVersion <- installed.packages()["DAPAR","Version"]
ProstarVersion <- installed.packages()["Prostar","Version"]
text <- paste("<strong>To cite DAPAR and ProStaR software:</strong><br>
S. Wieczorek, F. Combes, C. Lazar, Q. Giai-Gianetto,
L. Gatto, A. Dorffer, A.-M. Hesse, Y. Coute, M. Ferro,
C. Bruley, T. Burger. <i>\"DAPAR & ProStaR: software to
perform statistical analyses in quantitative discovery
proteomics\"</i>, <i>Bioinformatics</i>, 2016
<br><br><br>
<strong>DAPAR</strong> and <strong>ProStaR</strong> form a
software suite for quantitative analysis of mass spectrometry
based proteomics, more specifically designed to process
relative quantitative data from discovery experiments.<br> <br>
It is composed of two distinct R packages : <br>",
"<ul style=\"list-style-type:disc;\">
<li>
<a href=\"http://www.bioconductor.org/packages/release/bioc/html/Prostar.html\"
title=\"here\" target=\"_blank\">Prostar</a> (version ",
ProstarVersion, "): the web based graphical user interface to DAPAR
</li>
<li>
<a href=\"http://www.bioconductor.org/packages/release/bioc/html/DAPAR.html\"
title=\"here\" target=\"_blank\">DAPAR</a> (version ",daparVersion,"): a
collection of tools and graphs dedicated to proteomic analysis
</li>
</ul>
In addition, it is bind to numerous other R packages available on
<a href=\"the https://cran.r-project.org/\" title=\"here\" target=\"_blank\">
CRAN</a> or on the <a href=\"http://www.bioconductor.org\"
title=\"here\" target=\"_blank\">Bioconductor</a>, among which
<a href=\"http://www.bioconductor.org/packages/release/bioc/html/MSnbase.html\"
title=\"here\" target=\"_blank\">MSnbase</a>, which has introduced Msnsets,
the data structure on which all the processing are based.
<br>
Here is a brief overview of the available functionalities:
<ul style=\"list-style-type:disc;\">
<li>
Descriptive statistics are available, for exploration and visualization of the
quantitative dataset;
</li>
<li>
Filtering options allows pruning the protein or peptide list according to
various criteria (missing values, contaminants, reverse sequences);
</li>
<li>
Cross replicate normalization, so as to make the quantitative
values comparable between the different analyzed samples;
</li>
<li>
Missing values imputation with different methods, depending
on the nature of the missing values;
</li>
<li>
Differential analysis, which includes null hypothesis
significance testing as well as multiple testing correction
(for false discovery rate estimation).
</li>
</ul>
<br>
<br>
For more details, please refer to the \"Help\" tab.", sep="")
HTML(text)
})
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