Skip to content

GitLab

Commit 1872f4d0 authored by Eugenie Lohmann's avatar Eugenie Lohmann 🎨
Browse files

change module by action with xargs sed

parent e77d32e9
Expand all Hide whitespace changes
Inline Side-by-side
Showing with 84 additions and 2066 deletions
AnalyCyte--Simplify-Your-Post-Analysis-Reporting-for-Cytometry.tex
View file @ 1872f4d0
......@@ -478,10 +478,10 @@ including how to create an account, log in, and navigate the interface.
Describe the Shiny framework used in the app and its benefits for
creating interactive web applications.
\hypertarget{sec-module-list}{%
\chapter{Module list}\label{sec-module-list}}
\hypertarget{sec-action-list}{%
\chapter{Module list}\label{sec-action-list}}
List and explain the different Shiny modules available in the app, along
List and explain the different Shiny actions available in the app, along
with their functions and usage.
\part{}
......
_metadata.yml 0 → 100644
View file @ 1872f4d0
page-navigation: false
\ No newline at end of file
_quarto.yml
View file @ 1872f4d0
......@@ -19,7 +19,7 @@ book:
- qmd/install.qmd
- qmd/users_how_to_start.qmd
- qmd/users_shiny_description.qmd
- qmd/users_shiny_module_list.qmd
- qmd/users_shiny_action_list.qmd
- qmd/users_shiny_file_type.qmd
- part: "Import"
chapters:
......@@ -60,9 +60,21 @@ format:
code-link: true
mermaid:
theme: neutral
prefer-html: true
epub:
cover-image: dessin-pipe2.svg
pdf:
documentclass: scrreprt
include-in-header:
text: |
\usepackage{makeidx}
\makeindex
include-after-body:
text: |
\printindex
prefer-html: true
lightbox: true
editor: visual
number-depth: 4
\ No newline at end of file
analycyte-manual.tex
View file @ 1872f4d0
......@@ -413,8 +413,8 @@ docker run -d -p 80:3838 \
\hypertarget{sec-shiny-workflow}{%
\chapter{Shiny workflow}\label{sec-shiny-workflow}}
\hypertarget{sec-module-list}{%
\chapter{Module list}\label{sec-module-list}}
\hypertarget{sec-action-list}{%
\chapter{Module list}\label{sec-action-list}}
\part{Import data}
......
docs/AnalyCyte--Simplify-Your-Post-Analysis-Reporting-for-Cytometry.epub 0 → 100644
View file @ 1872f4d0
File added
docs/AnalyCyte--Simplify-Your-Post-Analysis-Reporting-for-Cytometry.pdf
View file @ 1872f4d0
No preview for this file type
docs/index.html
View file @ 1872f4d0
......@@ -22,26 +22,7 @@ ul.task-list li input[type="checkbox"] {
margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */
vertical-align: middle;
}
/* CSS for citations */
div.csl-bib-body { }
div.csl-entry {
clear: both;
}
.hanging-indent div.csl-entry {
margin-left:2em;
text-indent:-2em;
}
div.csl-left-margin {
min-width:2em;
float:left;
}
div.csl-right-inline {
margin-left:2em;
padding-left:1em;
}
div.csl-indent {
margin-left: 2em;
}</style>
</style>
<script src="site_libs/quarto-nav/quarto-nav.js"></script>
......@@ -51,7 +32,6 @@ div.csl-indent {
<script src="site_libs/quarto-search/fuse.min.js"></script>
<script src="site_libs/quarto-search/quarto-search.js"></script>
<meta name="quarto:offset" content="./">
<link href="./qmd/preface.html" rel="next">
<script src="site_libs/quarto-html/quarto.js"></script>
<script src="site_libs/quarto-html/popper.min.js"></script>
<script src="site_libs/quarto-html/tippy.umd.min.js"></script>
......@@ -178,7 +158,7 @@ div.csl-indent {
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./qmd/users_shiny_module_list.html" class="sidebar-item-text sidebar-link">
<a href="./qmd/users_shiny_action_list.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Module list</span></span></a>
</div>
</li>
......@@ -380,40 +360,10 @@ div.csl-indent {
<h2 class="unnumbered anchored" data-anchor-id="welcome">Welcome</h2>
<div class="justify">
<p>AnalyCyte is an <code>shiny application</code> designed to improve post-analysis for cytometry data and user control over this process. This tool simplifies the workflow and facilitate effective decision-making in research and clinical settings. Users can manage their analyses independently, thanks to customized, modular standardized reports.</p>
<p>The tool supports data export from <a href="https://www.omiq.ai/">OMIQ</a> and <a href="https://www.flowjo.com/">FlowJo</a>, as well as data import as Excel spreadsheets. All R objects generated by the application can be easily re-executed to incorporate more recent modules.</p>
<section id="conventions-used-in-this-book" class="level3">
<h3 class="anchored" data-anchor-id="conventions-used-in-this-book">Conventions Used in This Book</h3>
<p>To comment or ask technical questions about this book, please <a href="https://gitcrcm.marseille.inserm.fr/lohmann/analycyte.book/-/issues/new">file an issue</a>.</p>
</section>
<section id="development-background" class="level3 unnumbered">
<h3 class="unnumbered anchored" data-anchor-id="development-background">Development Background</h3>
<p>The AnalyCyte web application was developed by the <a href="https://cibi.marseille.inserm.fr/">CiBi</a> platform at the Centre de Recherche en Cancérologie de Marseille (<a href="https://www.crcm-marseille.fr/">CRCM</a>).</p>
<p>We extend our sincere thanks to the Institut Français de Bioinformatique (<a href="https://www.france-bioinformatique.fr/en/home/">IFB</a>) for providing the <a href="https://biosphere.france-bioinformatique.fr/cloud/">deployment solutions</a> that have been instrumental in the successful launch and operation of our work.</p>
</section>
<section id="acknowledgments" class="level3">
<h3 class="anchored" data-anchor-id="acknowledgments">Acknowledgments</h3>
<!-- Thanks to CiBi platform -->
<!-- Thanks to DISC for hosting -->
<!-- Thanks to the IFB for the technical resources -->
<!-- Thanks to the CRCM cytometry platform, to the cytometrists who tested the application and for their feedback -->
<p>Thanks to the&nbsp;<code>projects</code>&nbsp; library&nbsp; <span class="citation" data-cites="projects">Krieger, Perzynski, and Dalton (<a href="qmd/references.html#ref-projects" role="doc-biblioref">2021</a>)</span> work on <a href="https://github.com/ClevelandClinicQHS/projects">Github</a></p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
</section>
<p>The tool supports data export from <a href="https://www.omiq.ai/">OMIQ</a> and <a href="https://www.flowjo.com/">FlowJo</a>, as well as data import as Excel spreadsheets. All R objects generated by the application can be easily re-executed to incorporate more recent actions.</p>
</div>
<div id="refs" class="references csl-bib-body hanging-indent" role="list" style="display: none">
<div id="ref-projects" class="csl-entry" role="listitem">
Krieger, Nik, Adam Perzynski, and Jarrod Dalton. 2021. <em>Projects: A Project Infrastructure for Researchers</em>. <a href="https://CRAN.R-project.org/package=projects">https://CRAN.R-project.org/package=projects</a>.
</div>
</div>
</section>
</main> <!-- /main -->
......@@ -863,15 +813,6 @@ window.document.addEventListener("DOMContentLoaded", function (event) {
}
});
</script>
<nav class="page-navigation">
<div class="nav-page nav-page-previous">
</div>
<div class="nav-page nav-page-next">
<a href="./qmd/preface.html" class="pagination-link">
<span class="nav-page-text">Preface</span> <i class="bi bi-arrow-right-short"></i>
</a>
</div>
</nav>
</div> <!-- /content -->
......
docs/qmd/a1-flowjo.html
View file @ 1872f4d0
......@@ -158,7 +158,7 @@ ul.task-list li input[type="checkbox"] {
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../qmd/users_shiny_module_list.html" class="sidebar-item-text sidebar-link">
<a href="../qmd/users_shiny_action_list.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Module list</span></span></a>
</div>
</li>
......
docs/qmd/a2-omiq.html
View file @ 1872f4d0
......@@ -158,7 +158,7 @@ ul.task-list li input[type="checkbox"] {
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../qmd/users_shiny_module_list.html" class="sidebar-item-text sidebar-link">
<a href="../qmd/users_shiny_action_list.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Module list</span></span></a>
</div>
</li>
......
docs/qmd/a3-analycyte-verse.html
View file @ 1872f4d0
......@@ -158,7 +158,7 @@ ul.task-list li input[type="checkbox"] {
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../qmd/users_shiny_module_list.html" class="sidebar-item-text sidebar-link">
<a href="../qmd/users_shiny_action_list.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Module list</span></span></a>
</div>
</li>
......
docs/qmd/a4-sec_mod_deploy_ifb.html
View file @ 1872f4d0
......@@ -158,7 +158,7 @@ ul.task-list li input[type="checkbox"] {
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../qmd/users_shiny_module_list.html" class="sidebar-item-text sidebar-link">
<a href="../qmd/users_shiny_action_list.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Module list</span></span></a>
</div>
</li>
......
docs/qmd/a5-yaml-parameters.html
View file @ 1872f4d0
......@@ -157,7 +157,7 @@ ul.task-list li input[type="checkbox"] {
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../qmd/users_shiny_module_list.html" class="sidebar-item-text sidebar-link">
<a href="../qmd/users_shiny_action_list.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Module list</span></span></a>
</div>
</li>
......
docs/qmd/export.html deleted 100644 → 0
View file @ e77d32e9
This diff is collapsed.
docs/qmd/glossary.html
View file @ 1872f4d0
......@@ -158,7 +158,7 @@ ul.task-list li input[type="checkbox"] {
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../qmd/users_shiny_module_list.html" class="sidebar-item-text sidebar-link">
<a href="../qmd/users_shiny_action_list.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Module list</span></span></a>
</div>
</li>
......
docs/qmd/html_files.html
View file @ 1872f4d0
......@@ -177,7 +177,7 @@ div.csl-indent {
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../qmd/users_shiny_module_list.html" class="sidebar-item-text sidebar-link">
<a href="../qmd/users_shiny_action_list.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Module list</span></span></a>
</div>
</li>
......
docs/qmd/import.html deleted 100644 → 0
View file @ e77d32e9
This diff is collapsed.
docs/qmd/install.html
View file @ 1872f4d0
......@@ -158,7 +158,7 @@ ul.task-list li input[type="checkbox"] {
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../qmd/users_shiny_module_list.html" class="sidebar-item-text sidebar-link">
<a href="../qmd/users_shiny_action_list.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Module list</span></span></a>
</div>
</li>
......
docs/qmd/loaded.html deleted 100644 → 0
View file @ e77d32e9
This diff is collapsed.
docs/qmd/preface.html
View file @ 1872f4d0
......@@ -20,7 +20,26 @@ ul.task-list li input[type="checkbox"] {
margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */
vertical-align: middle;
}
</style>
/* CSS for citations */
div.csl-bib-body { }
div.csl-entry {
clear: both;
}
.hanging-indent div.csl-entry {
margin-left:2em;
text-indent:-2em;
}
div.csl-left-margin {
min-width:2em;
float:left;
}
div.csl-right-inline {
margin-left:2em;
padding-left:1em;
}
div.csl-indent {
margin-left: 2em;
}</style>
<script src="../site_libs/quarto-nav/quarto-nav.js"></script>
......@@ -158,7 +177,7 @@ ul.task-list li input[type="checkbox"] {
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../qmd/users_shiny_module_list.html" class="sidebar-item-text sidebar-link">
<a href="../qmd/users_shiny_action_list.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Module list</span></span></a>
</div>
</li>
......@@ -350,9 +369,39 @@ ul.task-list li input[type="checkbox"] {
<p>The insights gleaned from these analyses are vital for comparing different experimental or clinical conditions and for identifying clusters that exhibit significant variations. However, the current identification methods are often limited, relying on statistical software that is not conducive to automation. This limitation complicates the generation of a list of candidate clusters, particularly when establishing a score that optimally combines multiple pieces of information.</p>
<p>In light of these challenges, post-clustering analysis with AnalyCyte becomes a powerful tool for cytometrists, enabling them to work autonomously and efficiently. By providing standardized reports tailored to specific comparisons, cytometrists can independently manage their analyses, fostering a deeper understanding of their data.</p>
<p>As we move towards more complex, high-dimensional data sets, the ability to consistently interpret and compare results becomes increasingly critical. Standardization paves the way for the development of new computational tools and automated analysis methods, which can handle the complexity of modern cytometry data while maintaining the quality and reliability of the results.</p>
<section id="conventions-used-in-this-book" class="level3">
<h3 class="anchored" data-anchor-id="conventions-used-in-this-book">Conventions Used in This Book</h3>
<p>To comment or ask technical questions about this book, please <a href="https://gitcrcm.marseille.inserm.fr/lohmann/analycyte.book/-/issues/new">file an issue</a>.</p>
</section>
<section id="development-background" class="level3 unnumbered">
<h3 class="unnumbered anchored" data-anchor-id="development-background">Development Background</h3>
<p>The AnalyCyte web application was developed by the <a href="https://cibi.marseille.inserm.fr/">CiBi</a> platform at the Centre de Recherche en Cancérologie de Marseille (<a href="https://www.crcm-marseille.fr/">CRCM</a>).</p>
<p>We extend our sincere thanks to the Institut Français de Bioinformatique (<a href="https://www.france-bioinformatique.fr/en/home/">IFB</a>) for providing the <a href="https://biosphere.france-bioinformatique.fr/cloud/">deployment solutions</a> that have been instrumental in the successful launch and operation of our work.</p>
</section>
<section id="acknowledgments" class="level3">
<h3 class="anchored" data-anchor-id="acknowledgments">Acknowledgments</h3>
<!-- Thanks to CiBi platform -->
<!-- Thanks to DISC for hosting -->
<!-- Thanks to the IFB for the technical resources -->
<!-- Thanks to the CRCM cytometry platform, to the cytometrists who tested the application and for their feedback -->
<p>Thanks to the&nbsp;<code>projects</code>&nbsp; library&nbsp; <span class="citation" data-cites="projects">Krieger, Perzynski, and Dalton (<a href="references.html#ref-projects" role="doc-biblioref">2021</a>)</span> work on <a href="https://github.com/ClevelandClinicQHS/projects">Github</a></p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
</section>
</div>
<div id="refs" class="references csl-bib-body hanging-indent" role="list" style="display: none">
<div id="ref-projects" class="csl-entry" role="listitem">
Krieger, Nik, Adam Perzynski, and Jarrod Dalton. 2021. <em>Projects: A Project Infrastructure for Researchers</em>. <a href="https://CRAN.R-project.org/package=projects">https://CRAN.R-project.org/package=projects</a>.
</div>
</div>
</main> <!-- /main -->
<script id="quarto-html-after-body" type="application/javascript">
......
docs/qmd/references.html
View file @ 1872f4d0
......@@ -177,7 +177,7 @@ div.csl-indent {
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../qmd/users_shiny_module_list.html" class="sidebar-item-text sidebar-link">
<a href="../qmd/users_shiny_action_list.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Module list</span></span></a>
</div>
</li>
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment