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<p style="margin-bottom: 0.5cm; line-height: 100%"><br/>
</p>
</div>
<p align="center" style="margin-bottom: 0cm; line-height: 100%"><font face="Arial, sans-serif"><font size="6" style="font-size: 28pt"><b>Shiny
ARC: Application web de parcours des données du projet</b></font></font></p>
<p class="western"> </p>
<p class="western"><font face="Arial, sans-serif">Objectifs de
l'application:</font></p>
<ul>
<li/>
<p class="western" style="margin-bottom: 0cm"><strong><font face="Arial, sans-serif">Faciliter</font></strong><font face="Arial, sans-serif">
le </font><strong><font face="Arial, sans-serif">partage</font></strong><font face="Arial, sans-serif">
de résultats </font>
</p>
<li/>
<p class="western" style="margin-bottom: 0cm"><strong><font face="Arial, sans-serif">Éviter
les modifications des documents </font></strong><font face="Arial, sans-serif">issus
d'analyse bio-informatique </font>
</p>
<li/>
<p class="western" style="margin-bottom: 0cm"><strong><font face="Arial, sans-serif">Filtrer
</font></strong><font face="Arial, sans-serif">les résultats
d'analyses du projet </font><strong><font face="Arial, sans-serif">MetSChem
in PDAC</font></strong><font face="Arial, sans-serif"> </font>
</p>
<li/>
<p class="western" style="margin-bottom: 0cm"><strong><font face="Arial, sans-serif">Visualiser</font></strong><font face="Arial, sans-serif">
les données </font>
</p>
<li/>
<p class="western"><strong><font face="Arial, sans-serif">Lancer
des Enrichissement </font></strong><font face="Arial, sans-serif">sur
une sélection de gènes d'intérêt</font></p>
</ul>
<p class="western" align="justify"> </p>
<p class="western" align="justify"><font face="Arial, sans-serif">Ce
site à été crée dans le cadre du projet PGA 2020 :
"Reprogrammation métabolique et chimiorésistance de
l'adénocarcinome pancréatique; Impact du dialogue cellules
tumorales-Microenvironnement". (2020-2022) Financement ANR.</font></p>
<p class="western" align="justify"><font face="Arial, sans-serif">Cahier
des charges rédigé en anglais:</font></p>
<table width="100%" cellpadding="4" cellspacing="0">
<col width="256*">
<tr>
<td width="100%" valign="top" style="border: 1px solid #000000; padding: 0.1cm">
<h1 class="western"><font face="Arial, sans-serif">ToR: Term of
Reference</font></h1>
<h3 class="western" align="justify" style="font-weight: normal"><font face="Arial, sans-serif">Dataset:</font></h3>
<p class="western" align="justify"><font face="Arial, sans-serif">The
datasets are the gene expression datasets generated according to
the RNA-seq and microarray protocols available on the git
<font color="#ce181e"><b>medschem-pdac-data-analysis</b></font> .
These protocols uses functions stored in the <font color="#ce181e"><b>MetSChemPDAC</b></font>
package. The data are stored in an R package named
<font color="#ce181e"><b>arcpga.data</b></font> as .Rda files
and usable directly by loading the package.</font></p>
<h3 class="western" align="justify" style="font-weight: normal"><font face="Arial, sans-serif">Definition:</font></h3>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif"><b>Application
shiny </b>: Shiny is an open source R package that provides an
elegant and powerful web framework for building web applications
using R.</font></p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif"><b>PDAC
</b>: Pancreatic ductal adenocarcinoma</font></p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif"><b>RDA
: </b></font><font face="Arial, sans-serif">The </font><font face="Arial, sans-serif"><b>RData</b></font><font face="Arial, sans-serif">
format (with extension . rda) is a format designed for use with
</font><font face="Arial, sans-serif"><b>R.</b></font><code class="western"><font face="Arial, sans-serif">The
most common location for package data is data/. Package .RData
file are created by save() containing a single object (with the
same name as the file). </font></code>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><br/>
</p>
<h3 class="western" align="justify" style="font-weight: normal"><font face="Arial, sans-serif">Entries:</font></h3>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif">The
shiny app use the </font><font color="#ce181e"><font face="Arial, sans-serif"><b>data
package arcpga.data</b></font></font><font face="Arial, sans-serif">
available at :
</font><font color="#000080"><u><a href="https://gitcrcm.marseille.inserm.fr/lohmann/arcpga.data"><font face="Arial, sans-serif">https://gitcrcm.marseille.inserm.fr/lohmann/arcpga.data</font></a></u></font><font face="Arial, sans-serif">
but will be able to deal new data provided by the user.</font></p>
<p class="western" align="justify" style="margin-bottom: 0cm"><br/>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><br/>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif">Typically
it will take as input :<font color="#21409a"> </font><font color="#21409a"><b>RNA-seq
</b></font><font color="#21409a"><b>normalized counts or
microarrays normalised data</b></font><font color="#21409a">
</font>(Column are sample IDs and each lines are different gene
entries.) and can add a <font color="#21409a"><b>differential
expression table</b></font> (with at least: logFC,Pvalue, FDR
columns, <b>groups to be compared</b>). Option to add the
<font color="#21409a"><b>Subselection</b></font><b> </b>of its
dataset. </font>
</p>
<h3 class="western" align="justify" style="font-weight: normal"><font face="Arial, sans-serif">Preintegrated
data: </font>
</h3>
<p class="western" align="justify" style="margin-bottom: 0cm">
<font face="Arial, sans-serif">- the microarray dataset
("<b>microarray.*</b>" in arcpga.data)</font></p>
<p class="western" align="justify" style="margin-bottom: 0cm">
<font face="Arial, sans-serif">- RNA-Seq mouse ("<b>rna.10090.*</b>"
in arcpga.data)</font></p>
<p class="western" align="justify" style="margin-bottom: 0cm">
<font face="Arial, sans-serif">- RNA-Seq humain ("<b>rna.9606.*</b>"
in arcpga.data)</font></p>
<p class="western" align="justify" style="margin-bottom: 0cm">
<font face="Arial, sans-serif">- CAF (coming soon)</font></p>
<p class="western" align="justify" style="margin-bottom: 0cm"><br/>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif">"<b>*.TMM.counts</b>"
: counts normalized. Column are sample IDs and lines are Gene
entries.</font></p>
<p class="western" align="justify" style="margin-bottom: 0cm"><a name="_GoBack"></a>
<br/>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif">"<b>*.topTable.<conditions></b>"
: (in arcpga.data data are sorted by adjusted pvalues)
differential analysis table. </font>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><br/>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif"><conditions>
are detailed in the list "<b>SubSelection</b>"
integrated in the arcpga.data package. It will be use to
retrieve normalized count in the TMM table. </font>
</p>
<p class="western" align="justify" style="margin-left: 1.25cm; margin-bottom: 0cm">
<br/>
</p>
<p class="western" align="justify" style="margin-left: 1.25cm; margin-bottom: 0cm">
<font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">SubSelection</font></font></p>
<p class="western" align="justify" style="margin-left: 1.25cm; margin-bottom: 0cm">
<font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">$BATCHS</font></font></p>
<p class="western" align="justify" style="margin-left: 1.25cm; margin-bottom: 0cm">
<font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">[1]
"F0" "F1" "F2" "F3"
Genes that could be link to batch effect</font></font></p>
<p class="western" align="justify" style="margin-left: 1.25cm; margin-bottom: 0cm">
<br/>
</p>
<p class="western" align="justify" style="margin-left: 1.25cm; margin-bottom: 0cm">
<font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">$`P9DCD
vs F2NT`</font></font></p>
<p class="western" align="justify" style="margin-left: 1.25cm; margin-bottom: 0cm">
<font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">[1]
"P9.F2.FOLX.DCD" "F2.NT.NT" Immediate
effect of folfixinox</font></font></p>
<p class="western" align="justify" style="margin-left: 1.25cm; margin-bottom: 0cm">
<br/>
</p>
<p class="western" align="justify" style="margin-left: 1.25cm; margin-bottom: 0cm">
<font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">$`F0NT
vs F1NT`</font></font></p>
<p class="western" align="justify" style="margin-left: 1.25cm; margin-bottom: 0cm">
<font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">[1]
"F0" "F1" Mouse effect</font></font></p>
<p class="western" align="justify" style="margin-left: 1.25cm; margin-bottom: 0cm">
<br/>
</p>
<p class="western" align="justify" style="margin-left: 1.25cm; margin-bottom: 0cm">
<font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">$`F2S
vs F2NT`</font></font></p>
<p class="western" align="justify" style="margin-left: 1.25cm; margin-bottom: 0cm">
<font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">[1]
"F2.FOLX.S" "F2.NT.NT" </font><font size="2" style="font-size: 10pt">Treatment
response </font></font>
</p>
<p class="western" align="justify" style="margin-left: 1.25cm; margin-bottom: 0cm">
<br/>
</p>
<p class="western" align="justify" style="margin-left: 1.25cm; margin-bottom: 0cm">
<font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">$`F2S
vs F3R`</font></font></p>
<p class="western" align="justify" style="margin-left: 1.25cm; margin-bottom: 0cm">
<font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">[1]
"F2.FOLX.S" "F3.FOLX.R" </font><font size="2" style="font-size: 10pt">Developpment
ChimioResistance</font></font></p>
<p class="western" align="justify" style="margin-left: 1.25cm; margin-bottom: 0cm">
<br/>
</p>
<p class="western" align="justify" style="margin-left: 1.25cm; margin-bottom: 0cm">
<font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">$`F3S
vs F3R`</font></font></p>
<p class="western" align="justify" style="margin-left: 1.25cm; margin-bottom: 0cm">
<font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">[1]
"F3.FOLX.S" "F3.FOLX.R" </font><font size="2" style="font-size: 10pt">Acquired
ChimioResistance</font></font></p>
<p class="western" align="justify" style="margin-left: 1.25cm; margin-bottom: 0cm">
<br/>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif">If
user don’t specify subselection for its dataset all TMM count
will be displayed.<b> </b></font>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><br/>
</p>
<p class="western" align="justify"><font face="Arial, sans-serif">Within
arcpga.data </font>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif"><b>GeneIDS</b>
: Table with Gene IDs "Hs.9606.EntrezID"
,"Mm.10090.ensembl_gene_id","Mm.10090.EntrezID"
, "Mm.10090.Symbol" ,"Hs.9606.ensembl_gene_id"
, "ProbeName","SystematicName"
,"Hs.9606.Symbol" included in arcpga.data</font></p>
<p class="western" align="justify" style="margin-bottom: 0cm">“<font face="Arial, sans-serif"><b>10090”</b>
identifies mouse Ids. </font>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm">“<font face="Arial, sans-serif">9606”
identifies humans. </font>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><br/>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif"><font color="#000000"><b>GIDlist</b></font><font color="#000000">
: R huge list (list of list of vectors). "</font><font color="#000000">Hs.</font><font color="#000000">9606.</font><font color="#000000"><b>EMT</b></font><font color="#000000">"
, "</font><font color="#000000">Hs.</font><font color="#000000">9606.</font><font color="#000000"><b>METABO</b></font><font color="#000000">"
, "</font><font color="#000000">Hs.</font><font color="#000000">9606.</font><font color="#000000"><b>THERAPY</b></font><font color="#000000">",
"</font><font color="#000000">Hs.</font><font color="#000000">9606.</font><font color="#000000"><b>EPIENZYME</b></font><font color="#000000">",
"</font><font color="#000000">Hs.</font><font color="#000000">9606.</font><font color="#000000"><b>SLC</b></font><font color="#000000">",
"</font><font color="#000000">Mm.</font><font color="#000000">10090.METABO"
, "</font><font color="#000000">Mm.</font><font color="#000000">10090.EMT","</font><font color="#000000">Mm.</font><font color="#000000">10090.EPIENZYME
, "</font><font color="#000000">Mm
.10090</font><font color="#000000">.</font><font color="#000000"><b>SLC</b></font><font color="#000000">","</font><font color="#000000">Mm.</font><font color="#000000">10090.THERAPY"</font></font></p>
<p class="western" align="justify" style="margin-bottom: 0cm"><br/>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif">"Hs.9606.F2P9DCDF2NT”:<b>Treatment
Imediate Response</b></font></p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif">"Hs.9606.F2SF2NT”:<b>Folx
Induced</b>" </font>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif">"Hs.9606.F2SF3R”:<b>Chimio
Resistance</b>" </font>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif">"Hs.9606.<b>Batch
Induced</b>" </font>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif">"Hs.9606.<b>Mouse
Effect</b>" are Entrez Gene list determined from the
microarray analysis </font>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><br/>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif">the
pre-integrated list are part of the ARC project, user will be able
to provide its own. The pre-integrated list are “EntrezIDs”,
it can be translate to others id types thanks to the GeneIDS table
from metSChemPDACdata.</font></p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif">If
a new gene list is provided and have no correspondence (ID not in
the dataset) genes Ids will be omitted. </font>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif">User
will be able to provide its preferred IDs ( EntrezId, Ensembl,
symbol... ). </font>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><a name="__DdeLink__339_3291128693"></a>
<font face="Arial, sans-serif"><b><</b><b>Mm.</b><b>10090.></b>
are pre-integrated mouse Entrez Ids,<b><</b><b>Hs.</b><b>9606.></b>
are humans Entrez Ids in GeneIDS table. </font>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><br/>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif">For
a complete list of arcpga.data data , use:</font></p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif">library(help
= "arcpga.data")</font></p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif"><font color="#000000">Raw
data used to generate those results will be made available in
arcpga.data/raw-data with code for reproducibility. </font></font>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><br/>
</p>
<h3 class="western" align="justify" style="font-weight: normal"><font face="Arial, sans-serif"><font color="#000000">Confidentiality
and Code</font><font color="#000000">:</font></font></h3>
<p class="western" align="justify" style="margin-bottom: 0cm"><br/>
</p>
<ul>
<li/>
<p class="western" align="justify" style="margin-bottom: 0cm">
<font face="Arial, sans-serif">Project on Gitlab CRCM </font>
</p>
</ul>
<p class="western" align="justify" style="margin-bottom: 0cm"><br/>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font color="#ce181e"><font face="Arial, sans-serif"><span lang="fr-FR"><b>arcpga.data</b></span></font></font><font face="Arial, sans-serif"><span lang="fr-FR">
(repos du package) :
</span></font><font color="#000080"><u><a href="https://gitcrcm.marseille.inserm.fr/lohmann/arcpga.data"><font face="Arial, sans-serif"><span lang="fr-FR">https://gitcrcm.marseille.inserm.fr/lohmann/arcpga.data</span></font></a></u></font><font face="Arial, sans-serif"><span lang="fr-FR">
need R>3.5 </span></font>
</p>
<p lang="fr-FR" class="western" align="justify" style="margin-bottom: 0cm">
<br/>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font color="#ce181e"><font face="Arial, sans-serif"><b>medschem-pdac-data-analysis</b></font></font><font face="Arial, sans-serif">
(Differential analysis and implementation of the package data) :
</font><font color="#000080"><u><a href="https://gitcrcm.marseille.inserm.fr/bidaut/medschem-pdac-data-analysis"><font face="Arial, sans-serif">https://gitcrcm.marseille.inserm.fr/bidaut/medschem-pdac-data-analysis</font></a></u></font><font face="Arial, sans-serif">
</font>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><br/>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font color="#ce181e"><font face="Arial, sans-serif"><b>MetSChemPDAC
</b></font></font><font face="Arial, sans-serif"> (R package
containing differential analysis functions and the shiny
application </font><font face="Arial, sans-serif"><b>MetSChemPDAC/inst/app</b></font><font face="Arial, sans-serif">
) : </font><font color="#000080"><u><a href="https://gitcrcm.marseille.inserm.fr/lohmann/MetSChemPDAC"><font face="Arial, sans-serif">https://gitcrcm.marseille.inserm.fr/lohmann/MetSChemPDAC</font></a></u></font><font face="Arial, sans-serif">
need R>2.5</font></p>
<p class="western" align="justify" style="margin-bottom: 0cm"><br/>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif"><b>Package
installation :</b></font></p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif">I
did not manage to use remotes::install_git() yet </font>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif">the
package can be cloned with https and then install with devtools </font>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><br/>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif">require(devtools)</font></p>
<p class="western" align="justify" style="margin-bottom: 0cm"><font face="Arial, sans-serif">devtools::install(<path_to_cloned_git></font><font face="Arial, sans-serif">)</font></p>
<p class="western" align="justify"><br/>
</p>
</td>
</tr>
</table>
<h1 class="western"></h1>
<h1 class="western"></h1>
<p class="western"> </p>
<h4 class="western" align="center"><font face="Arial, sans-serif"><strong>Merci
au centre de données pour l'informatique et le calcul scientifique
(DISC) qui acceuil la plateforme shiny.</strong></font></h4>
<p class="western" align="justify" style="margin-bottom: 0cm; line-height: 100%">
<br/>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm; line-height: 100%">
<br/>
</p>
<p class="western" align="justify" style="margin-bottom: 0cm; line-height: 100%">
<br/>
</p>
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