Commit 5695bbcf authored by Christian Arnold's avatar Christian Arnold
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Small website improvements: Linking to GRaNPA and adding Rim as author

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Package: GRaNIE
Title: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data
Version: 0.14.1
Version: 0.14.2
Encoding: UTF-8
Authors@R: c(person("Christian", "Arnold", email =
"christian.arnold@embl.de", role = c("cre","aut")),
person("Judith", "Zaugg", email =
"judith.zaugg@embl.de", role = c("aut")),
person("Rim", "Moussa", email =
"rim.moussa01@gmail.com", role = "ctb"),
"rim.moussa01@gmail.com", role = "aut"),
person("Armando", "Reyes-Palomares", email =
"armandorp@gmail.com", role = "ctb"),
person("Giovanni", "Palla", email =
......
......@@ -2,7 +2,7 @@
The companion packages *GRaNIE* (**G**ene **R**egul**a**tory **N**etwork **I**nference including **E**nhancers) and *GRaNPA* (**G**ene **R**egul**a**tory **N**etwork **P**erformace **A**nalysis) are currently under active development. If you have questions, please do not hesitate to contact us (see below).
This page describes *GRaNIE*. For *GRaNPA*, please visit [this page](https://git.embl.de/grp-zaugg/GRaNPA).
This page describes *GRaNIE*. For *GRaNPA*, please visit [this page](https://grp-zaugg.embl-community.io/GRaNPA).
### Summary
......
......@@ -38,7 +38,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.2</span>
</span>
</div>
......@@ -106,7 +106,7 @@ Content not found. Please use links in the navbar.
<footer><div class="copyright">
<p></p>
<p>Developed by Christian Arnold, Judith Zaugg.</p>
<p>Developed by Christian Arnold, Judith Zaugg, Rim Moussa.</p>
</div>
<div class="pkgdown">
......
......@@ -23,7 +23,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.2</span>
</span>
</div>
......@@ -94,7 +94,7 @@
<footer><div class="copyright">
<p></p><p>Developed by Christian Arnold, Judith Zaugg.</p>
<p></p><p>Developed by Christian Arnold, Judith Zaugg, Rim Moussa.</p>
</div>
<div class="pkgdown">
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......@@ -23,7 +23,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.2</span>
</span>
</div>
......@@ -79,7 +79,7 @@
</p>
</li>
<li>
<p><strong>Rim Moussa</strong>. Contributor.
<p><strong>Rim Moussa</strong>. Author.
</p>
</li>
<li>
......@@ -103,15 +103,15 @@
</div>
<p>Arnold C, Zaugg J (2021).
<p>Arnold C, Zaugg J, Moussa R (2021).
<em>GRaNIE: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data</em>.
R package version 0.14.1, <a href="https://grp-zaugg.embl-community.io/GRaNIE" class="external-link">https://grp-zaugg.embl-community.io/GRaNIE</a>.
R package version 0.14.2, <a href="https://grp-zaugg.embl-community.io/GRaNIE" class="external-link">https://grp-zaugg.embl-community.io/GRaNIE</a>.
</p>
<pre>@Manual{,
title = {GRaNIE: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data},
author = {Christian Arnold and Judith Zaugg},
author = {Christian Arnold and Judith Zaugg and Rim Moussa},
year = {2021},
note = {R package version 0.14.1},
note = {R package version 0.14.2},
url = {https://grp-zaugg.embl-community.io/GRaNIE},
}</pre>
......@@ -122,7 +122,7 @@ R package version 0.14.1, <a href="https://grp-zaugg.embl-community.io/GRaNIE" c
<footer><div class="copyright">
<p></p><p>Developed by Christian Arnold, Judith Zaugg.</p>
<p></p><p>Developed by Christian Arnold, Judith Zaugg, Rim Moussa.</p>
</div>
<div class="pkgdown">
......
......@@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.2</span>
</span>
</div>
......@@ -93,7 +93,7 @@
<h3 id="granie-and-granpa-inference-and-evaluation-of-enhancer-mediated-gene-regulatory-networks">GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks<a class="anchor" aria-label="anchor" href="#granie-and-granpa-inference-and-evaluation-of-enhancer-mediated-gene-regulatory-networks"></a>
</h3>
<p>The companion packages <em>GRaNIE</em> (<strong>G</strong>ene <strong>R</strong>egul<strong>a</strong>tory <strong>N</strong>etwork <strong>I</strong>nference including <strong>E</strong>nhancers) and <em>GRaNPA</em> (<strong>G</strong>ene <strong>R</strong>egul<strong>a</strong>tory <strong>N</strong>etwork <strong>P</strong>erformace <strong>A</strong>nalysis) are currently under active development. If you have questions, please do not hesitate to contact us (see below).</p>
<p>This page describes <em>GRaNIE</em>. For <em>GRaNPA</em>, please visit <a href="https://git.embl.de/grp-zaugg/GRaNPA" class="external-link">this page</a></p>
<p>This page describes <em>GRaNIE</em>. For <em>GRaNPA</em>, please visit <a href="https://grp-zaugg.embl-community.io/GRaNPA" class="external-link">this page</a>.</p>
</div>
<div class="section level3">
<h3 id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
......@@ -146,6 +146,7 @@
<ul class="list-unstyled">
<li>Christian Arnold <br><small class="roles"> Maintainer, author </small> </li>
<li>Judith Zaugg <br><small class="roles"> Author </small> </li>
<li>Rim Moussa <br><small class="roles"> Author </small> </li>
<li><a href="authors.html">More about authors...</a></li>
</ul>
</div>
......@@ -158,7 +159,7 @@
<footer><div class="copyright">
<p></p>
<p>Developed by Christian Arnold, Judith Zaugg.</p>
<p>Developed by Christian Arnold, Judith Zaugg, Rim Moussa.</p>
</div>
<div class="pkgdown">
......
......@@ -23,7 +23,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.2</span>
</span>
</div>
......@@ -154,7 +154,7 @@
<footer><div class="copyright">
<p></p><p>Developed by Christian Arnold, Judith Zaugg.</p>
<p></p><p>Developed by Christian Arnold, Judith Zaugg, Rim Moussa.</p>
</div>
<div class="pkgdown">
......
......@@ -5,5 +5,5 @@ articles:
Introduction: Introduction.html
quickStart: quickStart.html
workflow: workflow.html
last_built: 2021-12-14T15:33Z
last_built: 2021-12-15T09:07Z
......@@ -23,7 +23,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.2</span>
</span>
</div>
......@@ -65,7 +65,7 @@
</header><div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Create, represent, investigate, quantify and visualize enhancer-mediated gene regulatory networks (<code>eGRNs</code>)</h1>
<h1>Create, represent, investigate, quantify and visualize enhancer-mediated gene regulatory networks (<strong>eGRNs</strong>)</h1>
<div class="hidden name"><code>GRN-class.Rd</code></div>
</div>
......@@ -143,7 +143,7 @@
<footer><div class="copyright">
<p></p><p>Developed by Christian Arnold, Judith Zaugg.</p>
<p></p><p>Developed by Christian Arnold, Judith Zaugg, Rim Moussa.</p>
</div>
<div class="pkgdown">
......
......@@ -23,7 +23,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.2</span>
</span>
</div>
......@@ -79,7 +79,7 @@
</tr><tr><td>
<p><code><a href="GRN-class.html">GRN-class</a></code> </p>
</td>
<td><p>Create, represent, investigate, quantify and visualize enhancer-mediated gene regulatory networks (<code>eGRNs</code>)</p></td>
<td><p>Create, represent, investigate, quantify and visualize enhancer-mediated gene regulatory networks (<strong>eGRNs</strong>)</p></td>
</tr><tr><td>
<p><code><a href="GRaNIE.html">GRaNIE</a></code> </p>
</td>
......@@ -221,7 +221,7 @@
<footer><div class="copyright">
<p></p><p>Developed by Christian Arnold, Judith Zaugg.</p>
<p></p><p>Developed by Christian Arnold, Judith Zaugg, Rim Moussa.</p>
</div>
<div class="pkgdown">
......
......@@ -3,7 +3,7 @@
\docType{class}
\name{GRN-class}
\alias{GRN-class}
\title{Create, represent, investigate, quantify and visualize enhancer-mediated gene regulatory networks (\code{eGRNs})}
\title{Create, represent, investigate, quantify and visualize enhancer-mediated gene regulatory networks (\strong{eGRNs})}
\description{
The class \code{\linkS4class{GRN}} stores data and information related to our \code{eGRN} approach to construct enhancer-mediated gene regulatory networks out of open chromatin and RNA-Seq data. See the description below for more details, and \strong{visit our project website at https://grp-zaugg.embl-community.io/GRaNIE and have a look at the various Vignettes}.
}
......
---
title: "Workflow example"
author: "Christian Arnold, Judith Zaugg"
author: "Christian Arnold, Judith Zaugg, Rim Moussa"
date: "`r BiocStyle::doc_date()`"
package: "`r BiocStyle::pkg_ver('GRaNIE')`"
abstract: >
......
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