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### GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks
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://grp-zaugg.embl-community.io/GRaNPA).
<img src="man/figures/logo_398x413.png" align="right" />
### GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks
**We are soon submitting our `GRaNIE` and the associated `GRaNIEData` for being included on `Bioconductor`. Once we are accepted and the package is included in the stable release of `Bioconductor`, we will update the installation guidelines in the documentation.**
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://grp-zaugg.embl-community.io/GRaNPA).
**We are soon submitting our *GRaNIE* and the associated *GRaNIEData* for being included on *Bioconductor*. Once we are accepted and the package is included in the stable release of *Bioconductor*, we will update the installation guidelines in the documentation.**
**If you use our packages, please use the following citation (we will update it once the paper has been officially published):**
GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks applied to study macrophages. Aryan Kamal, Christian Arnold, Annique Claringbould, Rim Moussa, Neha Daga, Daria Nogina, Maksim Kholmatov, Nila Servaas, Sophia Mueller-Dott, Armando Reyes-Palomares, Giovanni Palla, Olga Sigalova, Daria Bunina, Caroline Pabst, Judith B. Zaugg. bioRxiv 2021.12.18.473290; doi: https://doi.org/10.1101/2021.12.18.473290
GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks applied to study macrophages. Aryan Kamal, Christian Arnold, Annique Claringbould, Rim Moussa, Neha Daga, Daria Nogina, Maksim Kholmatov, Nila
Servaas, Sophia Mueller-Dott, Armando Reyes-Palomares, Giovanni Palla, Olga Sigalova, Daria Bunina, Caroline Pabst, Judith B. Zaugg. bioRxiv 2021.12.18.473290; doi: https://doi.org/10.1101/2021.12.18.473290
### 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
specific, likely because the combinations of transcription factors (TFs) that are regulating a given enhancer have cell-type-specific activity. This TF activity can be quantified with existing tools such as *diffTF* and captures differences in
binding of a TF in open chromatin regions. Collectively, this forms an enhancer-mediated gene regulatory network (*eGRN*) with cell-type and
data-specific TF-RE and RE-gene links.
Here, we reconstruct such a *eGRN* using bulk RNAseq and open chromatin (e.g., using ATACseq or ChIPseq for open
chromatin marks) and optionally TF activity data. Our network contains different types of links, connecting TFs to
regulatory elements, the latter of which is connected to genes in the vicinity or within the same chromatin domain
(TAD). We use a statistical framework to assign empirical FDRs and weights to all links using a permutation-based
approach.
Since no widely accepted ground-truth dataset for assessing the constructed *eGRN* exists, we propose a novel
evaluation algorithm which is not using a ground-truth network and instead assesses a *eGRN* based on its
performance in predicting differential expression response. For this, we used a random forest regression model and
evaluate how well the *eGRN* links predict differential expression values based on differential TF activity. Overall, our
*eGRNs* consistently perform significantly better than corresponding randomized versions, showing that they capture
reliable links between TFs and their target genes. Our framework also allows us to benchmark and compare different
*eGRN* reconstruction algorithms.
Finally, we run our *eGRN* construction and evaluation pipeline on diverse datasets such as naive CD4-positive T cells
or an AML cohort and identified a set of cell-type specific TFs with crucial roles to predict differential gene expression
based on differential TF activity. The resulting core subnetwork has higher predictive power and enables a deeper
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 specific, likely because the combinations
of transcription factors (TFs) that are regulating a given enhancer have
cell-type-specific activity. This TF activity can be quantified with existing
tools such as *diffTF* and captures differences in binding of a TF in open
chromatin regions. Collectively, this forms an enhancer-mediated gene regulatory
network (*eGRN*) with cell-type and data-specific TF-RE and RE-gene links. Here,
we reconstruct such a *eGRN* using bulk RNAseq and open chromatin (e.g., using
ATACseq or ChIPseq for open chromatin marks) and optionally TF activity data.
Our network contains different types of links, connecting TFs to regulatory
elements, the latter of which is connected to genes in the vicinity or within
the same chromatin domain (TAD). We use a statistical framework to assign
empirical FDRs and weights to all links using a permutation-based approach.
Since no widely accepted ground-truth dataset for assessing the constructed
*eGRN* exists, we propose a novel evaluation algorithm which is not using a
ground-truth network and instead assesses a *eGRN* based on its performance in
predicting differential expression response. For this, we used a random forest
regression model and evaluate how well the *eGRN* links predict differential
expression values based on differential TF activity. Overall, our *eGRNs*
consistently perform significantly better than corresponding randomized
versions, showing that they capture reliable links between TFs and their target
genes. Our framework also allows us to benchmark and compare different *eGRN*
reconstruction algorithms. Finally, we run our *eGRN* construction and
evaluation pipeline on diverse datasets such as naive CD4-positive T cells or an
AML cohort and identified a set of cell-type specific TFs with crucial roles to
predict differential gene expression based on differential TF activity. The
resulting core subnetwork has higher predictive power and enables a deeper
understanding of the underlying regulatory programs
### Get help and contact us
If you have questions or comments, feel free to contact us. We will be happy to answer any questions related to this project as well as questions related to the software implementation. For method-related questions, contact Judith B. Zaugg (judith.zaugg@embl.de). For technical questions, contact Christian Arnold (christian.arnold@embl.de).
If you have questions or comments, feel free to contact us. We will be happy to
answer any questions related to this project as well as questions related to the
software implementation. For method-related questions, contact Judith B. Zaugg
(judith.zaugg@embl.de). For technical questions, contact Christian Arnold
(christian.arnold@embl.de).
If you have questions, doubts, ideas or problems, please use the [Gitlab Issue Tracker](https://git.embl.de/grp-zaugg/GRaNIE/issues). We will respond in a timely manner.
If you have questions, doubts, ideas or problems, please use the [Gitlab Issue
Tracker](https://git.embl.de/grp-zaugg/GRaNIE/issues). We will respond in a
timely manner.
### Contributions
- Originally developed by Armando Reyes-Palomares and subsequently modified by Giovanni Palla
- Christian Arnold then took over and added many improvements and extensions and converted it to a proper R package with the help of various people from the Zaugg Lab, particularly Rim Moussa.
\ No newline at end of file
- Originally developed by Armando Reyes-Palomares and subsequently modified by
Giovanni Palla
- Christian Arnold then took over and added many improvements and
extensions and converted it to a proper R package with the help of various
people from the Zaugg Lab, particularly Rim Moussa.
\ No newline at end of file
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<h1 data-toc-skip>Get Started with the <em>GRaNIE</em> packages from the Zaugg Lab</h1>
<h4 data-toc-skip class="author">Christian Arnold, Judith Zaugg</h4>
<h4 data-toc-skip class="date">20 January 2022</h4>
<h4 data-toc-skip class="date">21 January 2022</h4>
<div class="hidden name"><code>quickStart.Rmd</code></div>
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<p><strong>This vignette gives you a 1 minute summary of how to install and use our <em>GRaNIE</em> packages. For more details, check out the other Vignettes.</strong></p>
<p><strong>This vignette gives you a 1 minute summary of how to install and use our <code>GRaNIE</code> and the associated <code>GRaNIEData</code> package. For more details, check out the other Vignettes.</strong></p>
<div class="section level2">
<h2 id="install-the-packages">Install the packages<a class="anchor" aria-label="anchor" href="#install-the-packages"></a>
</h2>
<p>We are soon submitting our <code>GRaNIE</code> and the associated <code>GRaNIEData</code> for being included on <code>Bioconductor</code>. Once we are accepted and the package is included in the stable release of <code>Bioconductor</code>, we will update the installation guidelines here.</p>
<p>Until then, you may install the packages as follows:</p>
<div class="section level3">
<h3 id="stable-version-granie">Stable version: <em>GRaNIE</em><a class="anchor" aria-label="anchor" href="#stable-version-granie"></a>
<h3 id="stable-version">Stable version<a class="anchor" aria-label="anchor" href="#stable-version"></a>
</h3>
<p>Installing our <em>GRaNIE</em> packages is easy. Just execute the following line into <em>R</em>:</p>
<p>Installing our <code>GRaNIE</code> package is very easy. Just execute the following line into <code>R</code>:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://devtools.r-lib.org/" class="external-link">devtools</a></span><span class="op">)</span>
<span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/remote-reexports.html" class="external-link">install_gitlab</a></span><span class="op">(</span><span class="st">"grp-zaugg/GRaNIE"</span>, subdir <span class="op">=</span> <span class="st">"src/GRaNIE"</span>, host <span class="op">=</span> <span class="st">"git.embl.de"</span>, force <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
<p>If you receive an error message, make sure you installed the devtools package. If you don’t have it installed yet, just execute the following code into <em>R</em>:</p>
<p>If you receive an error message, make sure you installed the devtools package. If you don’t have it installed yet, just execute the following code into <code>R</code>:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"devtools"</span><span class="op">)</span></code></pre></div>
</div>
<div class="section level3">
<h3 id="development-version-graniedev">Development version: <em>GRaNIEdev</em><a class="anchor" aria-label="anchor" href="#development-version-graniedev"></a>
<h3 id="development-version">Development version<a class="anchor" aria-label="anchor" href="#development-version"></a>
</h3>
<p>To install the development version of our <em>GRN</em> package, simply do:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/remote-reexports.html" class="external-link">install_gitlab</a></span><span class="op">(</span><span class="st">"grp-zaugg/GRaNIE"</span>, subdir <span class="op">=</span> <span class="st">"src/GRaNIEdev"</span>, host <span class="op">=</span> <span class="st">"git.embl.de"</span>, force <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
<p>At the moment, we do not recommend working with the development version, and only a selected number of people have access to it. If you want to be included, please contact us! We will update the instructions here once we change our policy.</p>
</div>
<div class="section level3">
<h3 id="data-package-graniedata">Data package: <em>GRaNIEData</em><a class="anchor" aria-label="anchor" href="#data-package-graniedata"></a>
<h3 id="data-package-graniedata">Data package: <code>GRaNIEData</code><a class="anchor" aria-label="anchor" href="#data-package-graniedata"></a>
</h3>
<p>Similarly, to install the <em>GRaNIEData</em> package, simply do:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<p>Similarly, to install the <code>GRaNIEData</code> package, simply do:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/remote-reexports.html" class="external-link">install_gitlab</a></span><span class="op">(</span><span class="st">"grp-zaugg/GRaNIE"</span>, subdir <span class="op">=</span> <span class="st">"src/GRaNIEData"</span>, host <span class="op">=</span> <span class="st">"git.embl.de"</span>, force <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
</div>
</div>
<div class="section level2">
<h2 id="what-do-the-different-packages-do">What do the different packages do?<a class="anchor" aria-label="anchor" href="#what-do-the-different-packages-do"></a>
</h2>
<p>The stable version <strong><em>GRaNIE</em></strong> package is the best choice for most users, it contains features that have been tested more thoroughly and that we provide support for.</p>
<p>The development version <strong><em>GRaNIEdev</em></strong> contains new features that may or may not be tested so far and we can only provide limited support for it. This is the version we actively work on, and every once in a while after finishing a new feature, we integrate it into the stable version in the <em>GRaNIE</em> package.</p>
<p>The <strong><em>GRaNIEdata</em></strong> package provides example data that can be used to test the package and run the Vignettes.</p>
<p>The stable package version is the best choice for most users, it contains features that have been tested more thoroughly and that we provide support for.</p>
<p>The development version contains new features that may or may not be tested so far and we can only provide limited support for it. This is the version we actively work on, and every once in a while after finishing a new feature, we integrate it into the stable version in the <code>GRaNIE</code> package.</p>
<p>The <code>GRaNIEData</code> package provides example data that can be used to test the package and run the Vignettes.</p>
</div>
<div class="section level2">
<h2 id="bug-reports-feature-requests-and-contact-information">Bug Reports, Feature Requests and Contact Information<a class="anchor" aria-label="anchor" href="#bug-reports-feature-requests-and-contact-information"></a>
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<!DOCTYPE html>
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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Authors and Citation • GRaNIE</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css"><script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"><script src="pkgdown.js"></script><meta property="og:title" content="Authors and Citation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-530L9SXFM1"></script><script>
......@@ -22,8 +22,8 @@
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">GRaNIEdev</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.4</span>
<a class="navbar-link" href="index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.5</span>
</span>
</div>
......@@ -104,14 +104,14 @@
<p>Arnold C, Zaugg J, Moussa R (2022).
<em>GRaNIEdev: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data</em>.
R package version 0.14.4, <a href="https://grp-zaugg.embl-community.io/GRaNIE" class="external-link">https://grp-zaugg.embl-community.io/GRaNIE</a>.
<em>GRaNIE: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data</em>.
R package version 0.14.5, <a href="https://grp-zaugg.embl-community.io/GRaNIE" class="external-link">https://grp-zaugg.embl-community.io/GRaNIE</a>.
</p>
<pre>@Manual{,
title = {GRaNIEdev: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data},
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 and Rim Moussa},
year = {2022},
note = {R package version 0.14.4},
note = {R package version 0.14.5},
url = {https://grp-zaugg.embl-community.io/GRaNIE},
}</pre>
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......@@ -5,7 +5,13 @@
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data • GRaNIEdev</title>
<title>GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data • GRaNIE</title>
<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png">
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......@@ -38,8 +44,8 @@
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">GRaNIEdev</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.4</span>
<a class="navbar-link" href="index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.5</span>
</span>
</div>
......@@ -89,12 +95,13 @@
</header><div class="row">
<div class="contents col-md-9">
<p><img src="reference/figures/logo_398x413.png" align="right"></p>
<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>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://grp-zaugg.embl-community.io/GRaNPA" class="external-link">this page</a>.</p>
<p><strong>Please use the following citation:</strong></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). 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>
<p><strong>We are soon submitting our <em>GRaNIE</em> and the associated <em>GRaNIEData</em> for being included on <em>Bioconductor</em>. Once we are accepted and the package is included in the stable release of <em>Bioconductor</em>, we will update the installation guidelines in the documentation.</strong></p>
<p><strong>If you use our packages, please use the following citation (we will update it once the paper has been officially published):</strong></p>
<p>GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks applied to study macrophages. Aryan Kamal, Christian Arnold, Annique Claringbould, Rim Moussa, Neha Daga, Daria Nogina, Maksim Kholmatov, Nila Servaas, Sophia Mueller-Dott, Armando Reyes-Palomares, Giovanni Palla, Olga Sigalova, Daria Bunina, Caroline Pabst, Judith B. Zaugg. bioRxiv 2021.12.18.473290; doi: <a href="https://doi.org/10.1101/2021.12.18.473290" class="external-link uri">https://doi.org/10.1101/2021.12.18.473290</a></p>
</div>
<div class="section level3">
......@@ -139,7 +146,7 @@
<div class="citation">
<h2 data-toc-skip>Citation</h2>
<ul class="list-unstyled">
<li><a href="authors.html#citation">Citing GRaNIEdev</a></li>
<li><a href="authors.html#citation">Citing GRaNIE</a></li>
</ul>
</div>
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......@@ -22,8 +22,8 @@
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">GRaNIEdev</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.4</span>
<a class="navbar-link" href="../index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.5</span>
</span>
</div>
......@@ -69,6 +69,81 @@
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="0.9-0.14" id="granie-09-014-2021-12-13">GRaNIE 0.9-0.14 (2021-12-13)<a class="anchor" aria-label="anchor" href="#granie-09-014-2021-12-13"></a></h2>
<div class="section level3">
<h3 id="major-changes-0-9-0-14">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-9-0-14"></a></h3>
<ul><li>major overhaul and continuous work on peak-gene QC plots</li>
<li>the <em>filterData</em> functions has now more filter parameters, such as filtering for CV. Also, all filters uniformly have a <em>min</em> and <em>max</em> filter.</li>
<li>integrated network statistics and various enrichment analyses</li>
<li>handling of edge cases and rare events in various functions</li>
<li>packages have been renamed to <em>GRaNIE</em> as basename (before: <em>GRN</em>)</li>
</ul></div>
<div class="section level3">
<h3 id="bug-fixes-0-9-0-14">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-0-14"></a></h3>
<ul><li>various minor bug fixes</li>
</ul></div>
<div class="section level3">
<h3 id="minor-changes-0-9-0-14">Minor changes<a class="anchor" aria-label="anchor" href="#minor-changes-0-9-0-14"></a></h3>
<ul><li>changed the object structure slightly and moved some gene and peak annotation data (such as mean, CV) to the appropriate annotation slot</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="0.8" id="granie-08-2021-05-07">GRaNIE 0.8 (2021-05-07)<a class="anchor" aria-label="anchor" href="#granie-08-2021-05-07"></a></h2>
<div class="section level3">
<h3 id="major-changes-0-8">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-8"></a></h3>
<ul><li>improved PCA plotting, PCA plots are now produced for both raw and normalized data</li>
<li>new filters for the function <em>filterGRaNIEAndConnectGenes</em> (<em>peak_gene.maxDistance</em>) as well as more flexibility how to adjust the peak-gene raw p-values for multiple testing (including the possibility to use IHW - experimental)</li>
<li>new function <em>plotDiagnosticPlots_TFPeaks</em> for plotting (this function was previously called only internally, but is now properly exported), in analogy to <em>plotDiagnosticPlots_peakGene</em>
</li>
</ul></div>
<div class="section level3">
<h3 id="bug-fixes-0-8">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-8"></a></h3>
<ul><li>various minor bug fixes (PCA plotting, compatibility when providing pre-normalized data)</li>
</ul></div>
<div class="section level3">
<h3 id="minor-changes-0-8">Minor changes<a class="anchor" aria-label="anchor" href="#minor-changes-0-8"></a></h3>
<ul><li>changed the object structure slightly and cleaned the config slot, for example</li>
<li>some functions have been added / renamed to make the workflow more clear and streamlined, see Vignette for details</li>
<li>some default parameters changed</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="0.7" id="granie-07-2021-03-12">GRaNIE 0.7 (2021-03-12)<a class="anchor" aria-label="anchor" href="#granie-07-2021-03-12"></a></h2>
<div class="section level3">
<h3 id="major-changes-0-7">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-7"></a></h3>
<ul><li>improved PCA plotting, also works for pre-normalized counts now when provided as input originally</li>
<li>more flexibility for data normalization</li>
<li>homogenized wordings, function calls and workflow clarity, removed unnecessary warnings when plotting peak-gene diagnostic plots, added more R help documentation</li>
<li>added IHW (Independent Hypothesis Weighting) as a multiple testing procedure for peak-gene p-values in addition to now allowing all methods that are supported by p.adjust</li>
</ul></div>
<div class="section level3">
<h3 id="bug-fixes-0-7">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-7"></a></h3>
<ul><li>various minor bug fixes</li>
</ul></div>
<div class="section level3">
<h3 id="minor-changes-0-7">Minor changes<a class="anchor" aria-label="anchor" href="#minor-changes-0-7"></a></h3>
</div>
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="0.6" id="granie-06-2021-02-09">GRaNIE 0.6 (2021-02-09)<a class="anchor" aria-label="anchor" href="#granie-06-2021-02-09"></a></h2>
<div class="section level3">
<h3 id="major-changes-0-6">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-6"></a></h3>
<ul><li>significant speed improvements for the peak-FDR calculations and subsequent plotting</li>
<li>TF-peak diagnostic plots now also show negatively correlated TF-peak statistics irrespective of whether they have been filtered out in the object / pipeline. This may be useful for diagnostic purposes to check whether excluding them is a sensible choice and to confirm the numbers are low</li>
</ul></div>
<div class="section level3">
<h3 id="bug-fixes-0-6">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-6"></a></h3>
<ul><li>Numbers for connections per correlation bin in the TF-peak diagnostic plots were wrong as they did not correctly differentiate between the different connection types in case multiple ones had been specified (e.g., expression and TF activity). This has been fixed.</li>
</ul></div>
<div class="section level3">
<h3 id="minor-changes-0-6">Minor changes<a class="anchor" aria-label="anchor" href="#minor-changes-0-6"></a></h3>
</div>
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="0.5" id="granie-05-2021-02-02">GRaNIE 0.5 (2021-02-02)<a class="anchor" aria-label="anchor" href="#granie-05-2021-02-02"></a></h2>
<p>first published package version</p>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
......
src/GRaNIE/docs/pkgdown.yml
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......@@ -5,5 +5,5 @@ articles:
packageDetails: packageDetails.html
quickStart: quickStart.html
workflow: workflow.html
last_built: 2022-01-20T21:41Z
last_built: 2022-01-21T11:22Z
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