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<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/38067?offset=200</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/28937/sushi-an-rbioconductor-package-for-visualizing-genomic-data</guid>
	<pubDate>Wed, 31 Aug 2016 08:29:12 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/28937/sushi-an-rbioconductor-package-for-visualizing-genomic-data</link>
	<title><![CDATA[Sushi: An R/Bioconductor package for visualizing genomic data]]></title>
	<description><![CDATA[<p>Sushi: An R/Bioconductor package for visualizing genomic data</p><p>Address of the bookmark: <a href="https://www.bioconductor.org/packages/devel/bioc/vignettes/Sushi/inst/doc/Sushi.pdf" rel="nofollow">https://www.bioconductor.org/packages/devel/bioc/vignettes/Sushi/inst/doc/Sushi.pdf</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<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>
<item>
	<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>
<item>
	<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/bookmarks/view/37732/making-2d-hilbert-curve</guid>
	<pubDate>Mon, 17 Sep 2018 05:43:35 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37732/making-2d-hilbert-curve</link>
	<title><![CDATA[Making 2D Hilbert Curve]]></title>
	<description><![CDATA[<p><a href="https://en.wikipedia.org/wiki/Hilbert_curve">Hilbert curve</a>&nbsp;is a type of space-filling curves that folds one dimensional axis into a two dimensional space, but still keeps the locality. It has advantages to visualize data with long axis in following two aspects:</p>
<ol>
<li>greatly improve resolution of the visualization fron n to&nbsp;<span><span><span><span><span><span><span>&radic;</span></span><span><span><span><span>n</span></span></span></span></span></span></span></span><span>n</span></span>;</li>
<li>easy to visualize clusters because generally data points in the axis will also be close in the 2D space.</li>
</ol>
<p>This package aims to provide an easy and flexible way to visualize data through Hilbert curve. The implementation and example figures are based on following sources:</p>
<ul>
<li><a href="http://mkweb.bcgsc.ca/hilbert/">http://mkweb.bcgsc.ca/hilbert/</a></li>
<li><a href="http://corte.si/posts/code/hilbert/portrait/index.html">http://corte.si/posts/code/hilbert/portrait/index.html</a></li>
<li><a href="http://bioconductor.org/packages/devel/bioc/html/HilbertVis.html">http://bioconductor.org/packages/devel/bioc/html/HilbertVis.html</a></li>
</ul><p>Address of the bookmark: <a href="https://bioconductor.org/packages/devel/bioc/vignettes/HilbertCurve/inst/doc/HilbertCurve.html" rel="nofollow">https://bioconductor.org/packages/devel/bioc/vignettes/HilbertCurve/inst/doc/HilbertCurve.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</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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