Commit c4ab8d65 authored by Jerome Mariette's avatar Jerome Mariette

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......@@ -14,7 +14,7 @@
Karutha Pandian},
title = {Ultradeep 16S rRNA Sequencing Analysis of Geographically Similar
but Diverse Unexplored Marine Samples Reveal Varied Bacterial Community
Composition.},
Composition},
journal = {PLOS one},
year = {2013}
}
......@@ -24,23 +24,29 @@
Anna Capaldo and Anna Carleo and Alessandro Armini and Vincenzo De Leo and Paola Piomboni and
Riccardo Focarelli and Luca Bini},
title = {A methodological and functional proteomic approach of human follicular
fluid en route for oocyte quality evaluation.},
fluid en route for oocyte quality evaluation},
journal = {Journal of Proteomics},
year = {2013},
volume = {90},
pages = {6176}
pages = {61-76}
}
@ARTICLE{Dillies2012,
author = {Marie-Agnès Dillies, Andrea Rau, Julie Aubert, Christelle Hennequet-Antier, Marine Jeanmougin, Nicolas Servant, Céline Keime, Guillemette Marot, David Castel, Jordi Estelle, Gregory Guernec, Bernd Jagla, Luc Jouneau, Denis Laloë, Caroline Le Gall, Brigitte Schaëffer, Stéphane Le Crom, Mickaël Guedj and Florence Jaffrézic, on behalf of The French StatOmique Consortium},
title = {A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis.},
author = {Marie-Agnès Dillies and Andrea Rau and Julie Aubert and Christelle
Hennequet-Antier and Marine Jeanmougin and Nicolas Servant and Céline Keime and
Guillemette Marot and David Castel and Jordi Estelle and Gregory Guernec and
Bernd Jagla and Luc Jouneau and Denis Laloë and Caroline Le Gall and Brigitte
Schaëffer and Stéphane Le Crom and Mickaël Guedj and Florence Jaffrézic and on
behalf of The French StatOmique Consortium},
title = {A comprehensive evaluation of normalization methods for Illumina
high-throughput RNA sequencing data analysis},
journal = {Briefings in Bioinformatics},
year = {2012}
}
@ARTICLE{DeuPons2014,
author = {Jordi Deu-Pons and Michael P Schroeder and Nuria Lopez-Bigas},
title = {jHeatmap: an interactive heatmap viewer for the web.},
title = {jHeatmap: an interactive heatmap viewer for the web},
journal = {Bioinformatics},
year = {2014}
}
......@@ -58,7 +64,7 @@
@ARTICLE{Bronwen2012,
author = {Bronwen Martin and Wayne Chadwick and Tie Yi and Sung-Soo Park and Daoyuan Lu
and Bin Ni and Shekhar Gadkaree and Kathleen Farhang and Kevin G. Becker and Stuart Maudsley},
title = {VENNTUREA Novel Venn Diagram Investigational Tool for Multiple
title = {VENNTURE-A Novel Venn Diagram Investigational Tool for Multiple
Pharmacological Dataset Analysis },
journal = {PLoS ONE},
year = {2012}
......@@ -67,7 +73,7 @@
@ARTICLE{Lopes2010,
author = {Christian Lopes and Max Franz and Farzana Kazi and Sylva Donaldson
and Quaid Morris and Gary Bader},
title = {Cytoscape Web: an interactive web-based network browser.},
title = {Cytoscape Web: an interactive web-based network browser},
journal = {Bioinformatics},
year = {2010}
}
......@@ -77,7 +83,7 @@
Allias and G\'{e}rald Salin and C\'{e}line Noirot and Sylvain Thomas
and Christophe Klopp},
title = {NG6: Integrated next generation sequencing storage and processing
environment.},
environment},
journal = {BMC Genomics},
year = {2012}
}
......@@ -106,11 +112,12 @@
title = {RNAbrowse: RNA-seq de novo assembly results browser}
}
@OTHER{SanClemente,
@ARTICLE{SanClemente,
author = {Helene San Clemente and Elisabeth Jamet},
journal = {Database},
note = {in press},
title = {WallProtDB, a database resource for plant cell wall proteomics}
title = {WallProtDB, a database resource for plant cell wall proteomics},
year = {2014}
}
@ARTICLE{Venn1880,
......@@ -134,7 +141,7 @@
}
@OTHER{jquery,
title = {The write less, do more javascript library.},
title = {The write less, do more javascript library},
url = {http://jquery.com/}
}
......@@ -150,4 +157,4 @@
year = {2013},
title = {VennDiagram: Generate high-resolution Venn and Euler plots.},
url = {http://cran.r-project.org/web/packages/VennDiagram/index.html}
}
}
\ No newline at end of file
......@@ -352,11 +352,10 @@ provided by the user.
Venn diagrams are commonly used to present up to six lists but for six
lists, the intersection areas obtained when using a proportional layout are
often too small to
display the figures.
often too small to display the figures.
To display five or six lists diagrams, in a user-friendly manner, jvenn
implements several features (the user interface is provided in Fig.~\ref{fig::features}).
implements several features.
First, the layout can be switched between the standard layout and the
Edwards-Venn layout (Fig.~\ref{fig::edwards}) which gives a clearer graphical
representation for six lists diagrams. To enhance the figure's readability for
......@@ -502,9 +501,9 @@ and CK wrote the manuscript. All authors read and approved the final manuscript.
\section*{Acknowledgements}
We would like to acknowledge all our users for providing us useful feedback on
the system and for pointing out features worth developing. We thank the
reviewers for their insightful and constructive comments. We also thank Julie
Aubert and the French StatOmique Consortium for providing us the data used in
the ``Results'' section.
reviewers and Nathalie Villa-Vialaneix for their insightful and constructive
comments. We also thank Julie Aubert and the French StatOmique Consortium for
providing us the data used in the ``Results'' section.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% The Bibliography %%
......@@ -547,25 +546,34 @@ the ``Results'' section.
\section*{Figures}
\begin{figure}[h!]
\caption{\csentence{A six lists classic Venn diagram.}
This Venn diagram displays overlaps between six different biological
samples. The icon, located on the top-right, allows users to download the
diagram as a PNG file. The middle-right switch button
panel allows to activate or dis-activate lists to access a specific
intersection count. Charts showing the list size and intersection size
repartition located underneath the diagram.}\label{fig::features}
On mouse over a figure, the shape corresponding to the lists involved in
the intersection are highlighted and the other ones faded out. In
this example, the user pointed the intersection between DESeq, FQ, UQ and
TMM which contains 484 different genes.
}\label{fig::features}
\end{figure}
\begin{figure}[h!]
\caption{\csentence{A six lists Edwards-Venn diagram.}
On mouse over a figure, the shape corresponding to the lists involved in
the intersection are highlighted and the other ones faded out. In
this example, the user pointed the intersection between samples SRR068049,
SRR068051 and SRR068052 which contains eight different
items.}\label{fig::edwards}
This Venn diagram displays overlaps between six different biological
samples. The icon, located on the top-right, allows users to download the
diagram as a PNG file. The middle-right switch button
panel allows to activate or dis-activate lists to access a specific
intersection count. Charts showing the list size and intersection size
repartition located underneath the diagram.}\label{fig::edwards}
\end{figure}
\begin{figure}[h!]
\caption{\csentence{???.}???}\label{fig::web}
\caption{\csentence{jvenn web application.}
The running version of jvenn accessible at
http://bioinfo.genotoul.fr/jvenn/example.html. This one allows the user to
set all jvenn main features. The layout can be changed from classical to
Edwards, a search box is accessible, the switch button panel and the
exporting button are available and the statistical charts are displayed.
On the right of the page, each of the six textareas can be filled with a
list of elements (one per line). If the same item is given multiple times,
this one will be considered as unique. The list labels can also be customized
using the text field on the top of each textarea.}\label{fig::web}
\end{figure}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
......
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