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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/37732?offset=60</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/29638/r-graphical-cookbook-by-winston-chang</guid>
	<pubDate>Fri, 04 Nov 2016 12:50:30 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/29638/r-graphical-cookbook-by-winston-chang</link>
	<title><![CDATA[R Graphical Cookbook by Winston Chang]]></title>
	<description><![CDATA[<p>R Graphical Cookbook by Winston Chang</p><p>A very nice book by Winston Chang for R ethusiast. The R code presented in these pages is the R code actually used to produce the Figures in the book. There will be differences compared to the code chunks shown in the text of the book, but in most cases the differences will be that these pages contain additional code to lay out multiple plots on a single "page".</p><p>The code presented for each figure is self-contained, i.e., all code required to produce the figure is included. This means that there is sometimes considerable overlap of code between several figures  In some cases, it may be necessary to install an add-on package from CRAN to get the code to run.</p><p>More books at http://www.e-reading.club/bookreader.php/137370/C486x_APPb.pdf</p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/29638" length="37521" type="image/png" />
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32152/upsetr-shiny-app</guid>
	<pubDate>Fri, 14 Apr 2017 06:19:54 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32152/upsetr-shiny-app</link>
	<title><![CDATA[UpSetR Shiny App!]]></title>
	<description><![CDATA[<p>UpSetR generates static&nbsp;<a href="http://vcg.github.io/upset/?dataset=0&amp;duration=1000&amp;orderBy=subsetSize&amp;grouping=groupByIntersectionSize&amp;selection=">UpSet plots</a>. The UpSet technique visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such as the number of elements in the aggregates and intersections, as well as additional summary statistics derived from subset or element attributes.</p>
<h4>To begin, input your data using one of the three input styles.</h4>
<ol>
<li>"File" takes a correctly formatted.csv file.</li>
<li>"List" takes up to 6 different lists that contain unique elements, similar to that used in the web applications BioVenn&nbsp;<a href="http://www.biomedcentral.com/content/pdf/1471-2164-9-488.pdf">(Hulsen et al., 2008)</a>&nbsp;and jvenn&nbsp;<a href="http://www.biomedcentral.com/content/pdf/1471-2105-15-293.pdf">(Bardou et al., 2014)</a></li>
<li>"Expression" takes the input used by the venneuler R package&nbsp;<a href="https://cran.r-project.org/web/packages/venneuler/venneuler.pdf">(Wilkinson, 2015)</a></li>
</ol><p>Address of the bookmark: <a href="https://gehlenborglab.shinyapps.io/upsetr/" rel="nofollow">https://gehlenborglab.shinyapps.io/upsetr/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34041/r-tuorial</guid>
	<pubDate>Mon, 31 Jul 2017 08:41:40 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34041/r-tuorial</link>
	<title><![CDATA[R tuorial]]></title>
	<description><![CDATA[<p>R learning resources</p>
<p>https://flowingdata.com/</p><p>Address of the bookmark: <a href="https://flowingdata.com/" rel="nofollow">https://flowingdata.com/</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34585/r-googlevis-examples</guid>
	<pubDate>Sun, 10 Dec 2017 06:13:42 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34585/r-googlevis-examples</link>
	<title><![CDATA[R googleVis examples]]></title>
	<description><![CDATA[<p>It may take a little while to load all charts. Please be patient. All charts require an Internet connection.</p>
<p>These examples are taken from the googleVis demo. You can execute the demo via</p>
<pre><code><span>library</span><span>(</span><span>googleVis</span><span>)</span>
<span>demo</span><span>(</span><span>googleVis</span><span>)</span>
</code></pre>
<p>For more details about the charts and further examples see the helpfiles of the individual googleVis function and review the&nbsp;<a href="https://developers.google.com/chart/interactive/docs/gallery">Google Charts API documentation</a>&nbsp;and&nbsp;<a href="https://developers.google.com/terms">Terms of Service</a>.</p><p>Address of the bookmark: <a href="https://cran.r-project.org/web/packages/googleVis/vignettes/googleVis_examples.html" rel="nofollow">https://cran.r-project.org/web/packages/googleVis/vignettes/googleVis_examples.html</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/36585/custom-r-charts-coming-to-excel</guid>
	<pubDate>Sat, 12 May 2018 07:30:28 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/36585/custom-r-charts-coming-to-excel</link>
	<title><![CDATA[Custom R charts coming to Excel !]]></title>
	<description><![CDATA[<p>This week at the BUILD conference, Microsoft&nbsp;<a href="https://dev.office.com/blogs/azure-machine-learning-javascript-custom-functions-and-power-bi-custom-visuals-further-expand-developers-capabilities-with-excel" target="_blank">announced</a>&nbsp;that Power BI custom visuals will soon be available as charts with Excel. You'll be able to choose a range of data within an Excel workbook, and pass those data to one of the built-in Power BI custom visuals, or one you've&nbsp;<a href="https://github.com/Microsoft/PowerBI-Visuals/" target="_blank">created yourself using the API</a>.</p><p><a href="http://a0.typepad.com/6a0105360ba1c6970c0224e038fa08200d-pi" target="_blank"><img src="https://www.r-bloggers.com/wp-content/plugins/lazy-load/images/1x1.trans.gif" alt="Excel custom visuals" title="Excel custom visuals" style="border: 0px; border: 0px;"></a></p><p>Since you can&nbsp;<a href="https://docs.microsoft.com/en-us/power-bi/desktop-r-visuals?WT.mc_id=Revolutions-blog-davidsmi" target="_blank">create Power BI custom visuals using R</a>, that means you'll be able to design a custom R-based chart, and make it available to people using Excel &mdash; even if they don't know how to use R themselves. There also many&nbsp;<a href="https://appsource.microsoft.com/en-us/marketplace/apps?product=power-bi-visuals&amp;page=1&amp;src=office" target="_blank">pre-defined custom visuals available</a>, including some familiar R charts like&nbsp;<a href="https://appsource.microsoft.com/en-us/product/power-bi-visuals/WA104380817?tab=Overview" target="_blank">decision trees</a>,&nbsp;<a href="https://appsource.microsoft.com/en-us/product/power-bi-visuals/WA104380905?tab=Overview" target="_blank">calendar heatmaps</a>, and&nbsp;<a href="https://appsource.microsoft.com/en-us/product/power-bi-visuals/WA104381492?tab=Overview" target="_blank">hexbin scatterplots</a>.</p><p>For more details on how you'll be able to use custom R visuals in Excel, check out the blog post linked below.</p><p>PowerBI Blog:&nbsp;<a href="https://powerbi.microsoft.com/en-us/blog/excel-announces-new-data-visualization-capabilities-with-power-bi-custom-visuals/" target="_blank">Excel announces new data visualization capabilities with Power BI custom visuals</a></p>]]></description>
	<dc:creator>Surabhi Chaudhary</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/37610/applied-statistics-for-bioinformatics-using-r</guid>
	<pubDate>Thu, 30 Aug 2018 03:45:39 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/37610/applied-statistics-for-bioinformatics-using-r</link>
	<title><![CDATA[Applied Statistics for Bioinformatics using R]]></title>
	<description><![CDATA[<p>The purpose of this book is to give an introduction into statistics in order to solve some problems of bioinformatics. Statistics provides procedures to explore and visualize data as well as to test biological hypotheses. The book intends to be introductory in explaining and programming elementary statistical concepts, thereby bridging the gap between high school levels and the specialized statistical literature</p>]]></description>
	<dc:creator>Neel</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/37610" length="1368378" type="application/pdf" />
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38420/regioner-an-r-package-for-the-management-and-comparison-of-genomic-regions</guid>
	<pubDate>Tue, 11 Dec 2018 08:43:51 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38420/regioner-an-r-package-for-the-management-and-comparison-of-genomic-regions</link>
	<title><![CDATA[regioneR: an R package for the management and comparison of genomic regions]]></title>
	<description><![CDATA[<p><span>Regioner is an R package for the management and comparison of genomic regions. It offers a set of function for basic manipulation of region sets extending the functionality of GenomicRanges and a powerful and customizable permutation test framework. With it, it's possible to study the association of a set of regions with other sets of regions, functions defined over the genome or essentially any user defined function.</span></p>
<p><span>http://gattaca.imppc.org/regioner/</span></p><p>Address of the bookmark: <a href="http://gattaca.imppc.org/regioner/" rel="nofollow">http://gattaca.imppc.org/regioner/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39114/plumberan-r-package-that-converts-your-existing-r-code-to-a-web-api</guid>
	<pubDate>Wed, 13 Mar 2019 19:20:10 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39114/plumberan-r-package-that-converts-your-existing-r-code-to-a-web-api</link>
	<title><![CDATA[plumber:An R package that converts your existing R code to a web API]]></title>
	<description><![CDATA[<p>plumber allows you to create a REST API by merely decorating your existing R source code with special comments. Take a look at an example.</p>
<pre><code><span># plumber.R
</span><span>
</span><span>#* Echo back the input
#* @param msg The message to echo
#* @get /echo
</span><span>function</span><span>(</span><span>msg</span><span>=</span><span>""</span><span>){</span><span>
  </span><span>list</span><span>(</span><span>msg</span><span> </span><span>=</span><span> </span><span>paste0</span><span>(</span><span>"The message is: '"</span><span>,</span><span> </span><span>msg</span><span>,</span><span> </span><span>"'"</span><span>))</span><span>
</span><span>}</span><span>

</span><span>#* Plot a histogram
#* @png
#* @get /plot
</span><span>function</span><span>(){</span><span>
  </span><span>rand</span><span> </span><span>&lt;-</span><span> </span><span>rnorm</span><span>(</span><span>100</span><span>)</span><span>
  </span><span>hist</span><span>(</span><span>rand</span><span>)</span><span>
</span><span>}</span><span>

</span><span>#* Return the sum of two numbers
#* @param a The first number to add
#* @param b The second number to add
#* @post /sum
</span><span>function</span><span>(</span><span>a</span><span>,</span><span> </span><span>b</span><span>){</span><span>
  </span><span>as.numeric</span><span>(</span><span>a</span><span>)</span><span> </span><span>+</span><span> </span><span>as.numeric</span><span>(</span><span>b</span><span>)</span><span>
</span><span>}</span></code></pre><p>Address of the bookmark: <a href="https://www.rplumber.io/" rel="nofollow">https://www.rplumber.io/</a></p>]]></description>
	<dc:creator>BioJoker</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39947/radar-charts-with-ggplot2</guid>
	<pubDate>Tue, 17 Sep 2019 23:01:28 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39947/radar-charts-with-ggplot2</link>
	<title><![CDATA[radar charts with ggplot2]]></title>
	<description><![CDATA[<p><code>ggradar</code>&nbsp;allows you to build radar charts with ggplot2. This package is based on&nbsp;<a href="http://rstudio-pubs-static.s3.amazonaws.com/5795_e6e6411731bb4f1b9cc7eb49499c2082.html">Paul Williamson&rsquo;s</a>&nbsp;code, with new aesthetics and compatibility with ggplot2 2.0.</p>
<p>It was inspired by&nbsp;<a href="http://www.buildingwidgets.com/blog/2015/12/9/week-49-d3radarr">d3radaR</a>, an htmlwidget built by&nbsp;<a href="https://github.com/timelyportfolio">timelyportfolio</a>.</p><p>Address of the bookmark: <a href="https://github.com/ricardo-bion/ggradar" rel="nofollow">https://github.com/ricardo-bion/ggradar</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40583/trelliscope-flexibly-visualize-large-complex-data-in-great-detail-from-within-the-r-statistical-programming-environment</guid>
	<pubDate>Tue, 21 Jan 2020 04:22:49 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40583/trelliscope-flexibly-visualize-large-complex-data-in-great-detail-from-within-the-r-statistical-programming-environment</link>
	<title><![CDATA[Trelliscope: flexibly visualize large, complex data in great detail from within the R statistical programming environment.]]></title>
	<description><![CDATA[<p>Trelliscope provides a way to flexibly visualize large, complex data in great detail from within the R statistical programming environment. Trelliscope is a component in the<span>&nbsp;</span><a href="http://deltarho.org/docs-trelliscope/deltarho.org">DeltaRho</a><span>&nbsp;</span>environment.</p>
<p>For those familiar with<span>&nbsp;</span><a href="http://cm.bell-labs.com/cm/ms/departments/sia/project/trellis/">Trellis Display</a>,<span>&nbsp;</span><a href="http://docs.ggplot2.org/0.9.3.1/facet_wrap.html">faceting in ggplot</a>, or the notion of<span>&nbsp;</span><a href="http://en.wikipedia.org/wiki/Small_multiple">small multiples</a>, Trelliscope provides a scalable way to break a set of data into pieces, apply a plot method to each piece, and then arrange those plots in a grid and interactively sort, filter, and query panels of the display based on metrics of interest. With Trelliscope, we are able to create multipanel displays on data with a very large number of subsets and view them in an interactive and meaningful way.</p><p>Address of the bookmark: <a href="http://deltarho.org/docs-trelliscope/#introduction" rel="nofollow">http://deltarho.org/docs-trelliscope/#introduction</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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