Commit f0e5c2bc authored by Christian Arnold's avatar Christian Arnold
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Small website improvements: Linking to GRaNPA

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### GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks
*GRaNIE* (**G**ene **R**egul**a**tory **N**etwork **I**nference including **E**nhancers) is currently under active development. If you have questions, please do not hesitate to contact us (see below).
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).
### Summary
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</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="">0.14.1</span>
</span>
</div>
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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="">0.14.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.1</span>
</span>
</div>
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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="">0.14.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.1</span>
</span>
</div>
......@@ -105,13 +105,13 @@
<p>Arnold C, Zaugg J (2021).
<em>GRaNIE: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data</em>.
R package version 0.14.0, <a href="https://grp-zaugg.embl-community.io/GRaNIE" class="external-link">https://grp-zaugg.embl-community.io/GRaNIE</a>.
R package version 0.14.1, <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},
year = {2021},
note = {R package version 0.14.0},
note = {R package version 0.14.1},
url = {https://grp-zaugg.embl-community.io/GRaNIE},
}</pre>
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......@@ -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="">0.14.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.1</span>
</span>
</div>
......@@ -92,7 +92,8 @@
<div class="section level3">
<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><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) is currently under active development. If you have questions, please do not hesitate to contact us (see below).</p>
<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>
</div>
<div class="section level3">
<h3 id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
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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="">0.14.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.1</span>
</span>
</div>
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......@@ -5,5 +5,5 @@ articles:
Introduction: Introduction.html
quickStart: quickStart.html
workflow: workflow.html
last_built: 2021-12-14T14:22Z
last_built: 2021-12-14T15:33Z
......@@ -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="">0.14.1</span>
</span>
</div>
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### Gene Regulatory Network Inference including Enhancers: Reconstruction and evaluation of data-driven, cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNAseq data
### GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks
*GRaNIE* (**G**ene **R**egul**a**tory **N**etwork **I**nference including **E**nhancers) is currently under active development. If you have questions, please do not hesitate to contact us (see below).
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).
### Summary
*Towards a data-driven cell-type specific regulatory network including enhancers*
Genetic variants associated with diseases often affect non-coding regions, thus likely having a regulatory role. To
understand the effects of genetic variants in these regulatory regions, identifying genes that are modulated by specific
regulatory elements (REs) is crucial. The effect of gene regulatory elements, such as enhancers, is often cell-type
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