dysbiosisR/docs/index.html at master · microsud/dysbiosisR · GitHub

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    The dysbiosisR package implements tools for calculating some common dysbiosis
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    The dysbiosisR package implements tools for calculating some common dysbiosis
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<img src="logo.png" class="logo" alt=""><h1 id="dysbiosisr-">dysbiosisR <a class="anchor" aria-label="anchor" href="#dysbiosisr-"></a>
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<p>The <em>dysbiosisR</em> package is a collection of functions to calculate some common dysbiosis measures from microbiota profiling data. The package currently supports microbiome data organized as phyloseq objects.</p>
<div class="section level2">
<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
</h2>
<p>You can install the development version of <code>dysbiosisR</code> like this:</p>
<pre><code><span>    <span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"microsud/dysbiosisR"</span><span class="op">)</span></span></code></pre>
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<h2 id="load-package">Load package<a class="anchor" aria-label="anchor" href="#load-package"></a>
</h2>
<pre><code><span>    <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://github.com/microsud/dysbiosisR" class="external-link">dysbiosisR</a></span><span class="op">)</span></span></code></pre>
<p>The package is currently in the Beta version and a stable version will be made available soon. We welcome feedback and suggestions.</p>
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<h2 id="how-to-use">How to use<a class="anchor" aria-label="anchor" href="#how-to-use"></a>
</h2>
<p>Check out the <a href="https://microsud.github.io/dysbiosisR/articles/Introduction.html" class="external-link">dysbiosisR vignette</a> and <a href="https://microsud.github.io/dysbiosisR/reference/index.html" class="external-link">documentation of functions</a> for more details.</p>
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<h2 id="contribute">Contribute<a class="anchor" aria-label="anchor" href="#contribute"></a>
</h2>
<p>Contributions and feedback are very welcome:</p>
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<li><a href="https://github.com/microsud/dysbiosisR/issues" class="external-link">Raise Issue</a></li>
<li><a href="https://github.com/microsud/dysbiosisR" class="external-link">Star us on the Github page</a></li>
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<h2 id="cite">Cite<a class="anchor" aria-label="anchor" href="#cite"></a>
</h2>
<p>Shetty SA, et al., 2022. <em>dysbiosisR</em>: An R package to calculate common dysbiosis measures.</p>
<div class="section level3">
<h3 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
</h3>
<ol style="list-style-type: decimal">
<li><p>Santiago M, et al., 2019. Microbiome predictors of dysbiosis and VRE decolonization in patients with recurrent C. difficile infections in a multi-center retrospective study. AIMS Microbiol 5:1–18. 10.3934/microbiol.2019.1.1.</p></li>
<li><p>Lloyd-Price J, Arze C, Ananthakrishnan AN, et al., 2019. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 569:655–662. 10.1038/s41586-019-1237-9.</p></li>
<li><p>AlShawaqfeh MK, et al., 2017. A dysbiosis index to assess microbial changes in fecal samples of dogs with chronic inflammatory enteropathy. FEMS Microbiol Ecol 93:1–8. 10.1093/femsec/fix136.</p></li>
<li><p>Montassier E, Al-Ghalith GA, Hillmann B, Viskocil K, Kabage AJ, McKinlay CE, Sadowsky MJ, Khoruts A, Knights D. 2018. CLOUD: a non-parametric detection test for microbiome outliers. Microbiome 6:137. 10.1186/s40168-018-0514-4.</p></li>
<li><p>Saffouri GB, Shields-Cutler RR, Chen J, Yang Y, Lekatz HR, Hale VL, Cho JM, Battaglioli EJ, Bhattarai Y, Thompson KJ, Kalari KK, Behera G, Berry JC, Peters SA, Patel R, Schuetz AN, Faith JJ, Camilleri M, Sonnenburg JL, Farrugia G, Swann JR, Grover M, Knights D, Kashyap PC. 2019. Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders. Nat Commun 10:2012. 10.1038/s41467-019-09964-7.</p></li>
<li><p>Wei, S, Bahl, MI, Baunwall, SMD, Hvas, CL and Licht, TR. 2021. Determining gut microbial dysbiosis: a review of applied indexes for assessment of intestinal microbiota imbalances. Applied and Environmental Microbiology, 87(11), pp.e00395-21.</p></li>
<li><p>Halfvarson J, Brislawn CJ, Lamendella R, Vázquez-Baeza Y, Walters WA, Bramer LM, D’Amato M, Bonfiglio F, McDonald D, Gonzalez A, McClure EE, Dunklebarger MF, Knight R, Jansson JK. 2017. Dynamics of the human gut microbiome in inflammatory bowel disease. Nat Microbiol 2:17004. 10.1038/nmicrobiol.2017.4.</p></li>
</ol>
</div>
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<div class="section level2">
<h2 id="acknowledgement">Acknowledgement<a class="anchor" aria-label="anchor" href="#acknowledgement"></a>
</h2>
<p>This work was done at the Department of Medical Microbiology and Infection Prevention at UMC Groningen in collaboration with the Microbiome Group at the RIVM.</p>
</div>
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<h2 id="contact">Contact<a class="anchor" aria-label="anchor" href="#contact"></a>
</h2>
<p>Sudarshan A. Shetty (sudarshanshetty9[@]gmail[dot]com)<br>
Susana Fuentes (susana[dot]fuentes[@]rivm[dot]nl)</p>
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<h2 data-toc-skip>Developers</h2>
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<li>Sudarshan Shetty <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-5537-637X" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
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