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<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/44648?offset=150</link>
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	<description><![CDATA[]]></description>
	
	<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/38385/decipher-a-software-toolset-for-deciphering-and-managing-biological-sequences-efficiently-using-the-r</guid>
	<pubDate>Sun, 09 Dec 2018 19:06:17 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38385/decipher-a-software-toolset-for-deciphering-and-managing-biological-sequences-efficiently-using-the-r</link>
	<title><![CDATA[DECIPHER; a software toolset for deciphering and managing biological sequences efficiently using the R]]></title>
	<description><![CDATA[<p><span>DECIPHER is a software toolset that can be used for deciphering and managing biological sequences efficiently using the&nbsp;</span><a href="http://www.r-project.org/">R</a><span>&nbsp;programming language. The&nbsp;</span><a href="http://www.r-project.org/">R</a><span>&nbsp;package is distributed as platform independent source code under the&nbsp;</span><a href="http://www.gnu.org/copyleft/gpl.html">GPL version 3 license</a><span>. Some functionality of the program is accessible online through web tools.</span></p>
<p><span style="font-size: medium; text-align: justify;">&nbsp;</span></p><p>Address of the bookmark: <a href="http://www2.decipher.codes/" rel="nofollow">http://www2.decipher.codes/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38819/upsetr-an-r-package-for-the-visualization-of-intersecting-sets-and-their-properties</guid>
	<pubDate>Mon, 28 Jan 2019 18:38:44 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38819/upsetr-an-r-package-for-the-visualization-of-intersecting-sets-and-their-properties</link>
	<title><![CDATA[UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties]]></title>
	<description><![CDATA[<p>UpSetR generates static&nbsp;<a href="http://vcg.github.io/upset/">UpSet</a>&nbsp;plots. 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>
<p>For further details about the original technique see the&nbsp;<a href="http://vcg.github.io/upset/about/">UpSet website</a>. You can also check out the&nbsp;<a href="https://gehlenborglab.shinyapps.io/upsetr/">UpSetR shiny app</a>.&nbsp;<a href="https://github.com/hms-dbmi/UpSetR-shiny">Here is the source code</a>&nbsp;for the shiny wrapper.</p>
<p>A&nbsp;<a href="https://github.com/ImSoErgodic/py-upset">Python package</a>&nbsp;called&nbsp;<a href="https://github.com/ImSoErgodic/py-upset">py-upset</a>&nbsp;to create UpSet plots has been created by GitHub user&nbsp;<a href="https://github.com/ImSoErgodic">ImSoErgodic</a>.</p><p>Address of the bookmark: <a href="https://github.com/hms-dbmi/UpSetR/" rel="nofollow">https://github.com/hms-dbmi/UpSetR/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39884/retrieving-taxonomic-information-with-r</guid>
	<pubDate>Thu, 29 Aug 2019 01:38:39 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39884/retrieving-taxonomic-information-with-r</link>
	<title><![CDATA[Retrieving Taxonomic Information with R]]></title>
	<description><![CDATA[<p>This vignette will introduce users to the retrieval of taxonomic information with&nbsp;<code>myTAI</code>. The&nbsp;<code>taxonomy()</code>&nbsp;function implemented in&nbsp;<code>myTAI</code>&nbsp;relies on the powerful package&nbsp;<a href="https://github.com/ropensci/taxize">taxize</a>. Nevertheless, taxonomic information retrieval has been customized for the&nbsp;<code>myTAI</code>&nbsp;standard and for organism specific information retrieval.</p>
<p>Specifically, the&nbsp;<code>taxonomy()</code>&nbsp;function implemented in&nbsp;<code>myTAI</code>&nbsp;can be used to classify genomes according to phylogenetic classification into Phylostrata (Phylostratigraphy) or to retrieve species specific taxonomic information when performing Divergence Stratigraphy (see&nbsp;<a href="https://cran.r-project.org/web/packages/myTAI/vignettes/Introduction.html">Introduction</a>&nbsp;for details).</p><p>Address of the bookmark: <a href="https://cran.r-project.org/web/packages/myTAI/vignettes/Taxonomy.html" rel="nofollow">https://cran.r-project.org/web/packages/myTAI/vignettes/Taxonomy.html</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40463/%E2%80%98dockr%E2%80%99-the-r-container</guid>
	<pubDate>Mon, 23 Dec 2019 09:56:49 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40463/%E2%80%98dockr%E2%80%99-the-r-container</link>
	<title><![CDATA[‘dockr’: the R container]]></title>
	<description><![CDATA[<p><code>dockr</code> 0.8.6 is now available on CRAN. <code>dockr</code> is a minimal toolkit to build a lightweight Docker container image for your R package, in which the package itself is available. The Docker image seeks to mirror your R session as close as possible with respect to R specific dependencies. Both dependencies on CRAN R packages as well as local non-CRAN R packages will be included in the Docker container image.</p>
<p>If you want to know, how Docker works, and why you should consider using Docker, please take a look at the <a href="https://www.docker.com/why-docker" target="_blank">Docker website</a>.</p><p>Address of the bookmark: <a href="https://www.docker.com/why-docker" rel="nofollow">https://www.docker.com/why-docker</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40964/panev-an-r-package-for-a-pathway-based-network-visualization</guid>
	<pubDate>Sun, 09 Feb 2020 12:41:52 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40964/panev-an-r-package-for-a-pathway-based-network-visualization</link>
	<title><![CDATA[PANEV: an R package for a pathway-based network visualization]]></title>
	<description><![CDATA[<p><span>PANEV (PAthway NEtwork Visualizer) is an R package set for gene/pathway-based network visualization. Based on information available on KEGG, it visualizes genes within a network of multiple levels (from 1 to&nbsp;</span><em>n</em><span>) of interconnected upstream and downstream pathways. The network graph visualization helps to interpret functional profiles of a cluster of genes.</span></p>
<p><span><a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3371-7">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3371-7</a></span></p><p>Address of the bookmark: <a href="https://github.com/vpalombo/PANEV" rel="nofollow">https://github.com/vpalombo/PANEV</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41272/rainbowr-reliable-association-inference-by-optimizing-weights-with-r-r-package-for-snp-set-gwas-and-multi-kernel-mixed-model</guid>
	<pubDate>Fri, 28 Feb 2020 23:27:37 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41272/rainbowr-reliable-association-inference-by-optimizing-weights-with-r-r-package-for-snp-set-gwas-and-multi-kernel-mixed-model</link>
	<title><![CDATA[RAINBOWR: Reliable Association INference By Optimizing Weights with R (R package for SNP-set GWAS and multi-kernel mixed model)]]></title>
	<description><![CDATA[<p><code>RAINBOWR</code>(Reliable Association INference By Optimizing Weights with R) is a package to perform several types of <code>GWAS</code> as follows.</p>
<ul>
<li>Single-SNP GWAS with <code>RGWAS.normal</code> function</li>
<li>SNP-set (or gene set) GWAS with <code>RGWAS.multisnp</code> function (which tests multiple SNPs at the same time)</li>
<li>Check epistatic (SNP-set x SNP-set interaction) effects with <code>RGWAS.epistasis</code> (very slow and less reliable)</li>
</ul>
<p>https://github.com/KosukeHamazaki/RAINBOWR</p>
<p>https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007663</p>
<p>https://cran.r-project.org/web/packages/RAINBOWR/index.html</p><p>Address of the bookmark: <a href="https://github.com/KosukeHamazaki/RAINBOWR" rel="nofollow">https://github.com/KosukeHamazaki/RAINBOWR</a></p>]]></description>
	<dc:creator>Surabhi Chaudhary</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42299/platypus-%E2%80%93-r-package-for-object-detection-and-image-segmentation</guid>
	<pubDate>Mon, 09 Nov 2020 02:56:25 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42299/platypus-%E2%80%93-r-package-for-object-detection-and-image-segmentation</link>
	<title><![CDATA[Platypus – R package for object detection and image segmentation.]]></title>
	<description><![CDATA[<p><a href="https://github.com/maju116/platypus" target="_blank">platypus</a>&nbsp;is an R package for object detection and semantic segmentation. Currently using&nbsp;</p>
<div>platypus&nbsp;you can perform:</div>
<ul>
<li>multi-class semantic segmentation using&nbsp;U-Net&nbsp;architecture</li>
<li>multi-class object detection using&nbsp;YOLOv3&nbsp;architecture</li>
</ul>
<p>You can install the latest version of&nbsp;platypus&nbsp;with&nbsp;remotes&nbsp;package:</p>
<div>
<div>
<div>
<div>remotes::install_github("maju116/platypus")</div>
</div>
</div>
</div>
<p>Note that in order to install&nbsp;platypus&nbsp;you need to install&nbsp;keras&nbsp;and&nbsp;tensorflow&nbsp;packages and&nbsp;Tensorflow&nbsp;version&nbsp;&gt;= 2.0.0&nbsp;(&nbsp;Tensorflow 1.x&nbsp;will not be supported!)</p><p>Address of the bookmark: <a href="https://github.com/maju116/platypus" rel="nofollow">https://github.com/maju116/platypus</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>

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