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<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/21312?offset=1350</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34504/minion-gc-an-r-script-to-do-some-qc-on-minion-data</guid>
	<pubDate>Sun, 03 Dec 2017 15:19:18 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34504/minion-gc-an-r-script-to-do-some-qc-on-minion-data</link>
	<title><![CDATA[MinION_GC: An R script to do some QC on MinION data]]></title>
	<description><![CDATA[<p><span>Other tools focus on getting data out of the fastq or fast5 files, which is slow and computationally intensive. The benefit of this approach is that it works on a single, small, .txt summary file. So it's a lot quicker than most other things out there: it takes about a minute to analyse a 4GB flowcell on my laptop.</span></p>
<p>https://github.com/roblanf/minion_qc</p><p>Address of the bookmark: <a href="https://github.com/roblanf/minion_qc" rel="nofollow">https://github.com/roblanf/minion_qc</a></p>]]></description>
	<dc:creator>Radha Agarkar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/36418/r-350-has-been-released</guid>
	<pubDate>Thu, 26 Apr 2018 11:31:58 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/36418/r-350-has-been-released</link>
	<title><![CDATA[R 3.5.0 has been Released!]]></title>
	<description><![CDATA[<ul>
<li>The latest version of R is a major release! It comes with a ton of new features, including performance and speed improvements</li>
<li>All R packages will now be byte-compiled, hence boosting packages installed from GitHub</li>
<li>You may need to re-install all previously installed R packages; old scripts however will continue to work normally</li>
</ul><p>More at&nbsp;<a href="https://cran.r-project.org/doc/manuals/r-release/NEWS.html">https://cran.r-project.org/doc/manuals/r-release/NEWS.html</a></p>]]></description>
	<dc:creator>Jit</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>
<item>
	<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>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/41043/postdoctoral-scientist-genome-analytics-genome-bioinformatics-mf</guid>
  <pubDate>Sun, 16 Feb 2020 02:57:40 -0600</pubDate>
  <link></link>
  <title><![CDATA[Postdoctoral scientist genome analytics/ genome bioinformatics (m/f/*)]]></title>
  <description><![CDATA[
<p>https://www.uksh.de/jobs/Stellenangebote-nr-20190570-p-8.html<br />Your profile:<br />Degree in bioinformatics, biostatistics, or equivalent<br />Experience in the processing and analysis of large-scale genomics data using compute clusters / high-performance computing<br />Strong competence in working in Unix/Linux environments (shell)<br />Strong programming skills (in particular: Python, R, Perl)<br />Experience with using git and snakemake<br />Fluent English language skills, both spoken and written<br />Strong communication skills and motivation to work in a young, interdisciplinary, dynamic team</p>

<p>Additional Information:</p>

<p>If you have any questions about scientific aspects of this position, please contact Prof. Lars Bertram, head of LIGA (lars.bertram@uni-luebeck.de).</p>

<p>Please contact Ms. Anna Wolbert for further questions about administrative details (recruiting@uksh.de).</p>

<p>Weitere Informationen erhalten Sie auch unter www.uksh.de/karriere.</p>

<p>Wir freuen uns auf Ihre Bewerbung bis zum 15.03.2020 unter Angabe unserer Ausschreibungsnummer 20190570.119.CL.</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/41496/new-machine-learning-packages-in-r</guid>
	<pubDate>Fri, 27 Mar 2020 12:11:21 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/41496/new-machine-learning-packages-in-r</link>
	<title><![CDATA[New Machine Learning Packages in R]]></title>
	<description><![CDATA[<h3 id="machine-learning">Machine Learning</h3><p><a href="https://cran.r-project.org/package=autokeras">autokeras</a>&nbsp;v1.0.1: Implements an interface to&nbsp;<a href="https://autokeras.com/">AutoKeras</a>, an open source software library for automated machine learning. See&nbsp;<a href="https://cran.r-project.org/web/packages/autokeras/readme/README.html">README</a>&nbsp;for an example.</p><p><a href="https://cran.r-project.org/package=MTPS">MTPS</a>&nbsp;v0.1.9: Implements functions to predict simultaneous multiple outcomes based on revised stacking algorithms as described in&nbsp;<a href="denied:doi:10.1093/bioinformatics/btz531">Xing et al. (2019)</a>. See the&nbsp;<a href="https://cran.r-project.org/web/packages/MTPS/vignettes/Guide.html">vignette</a>&nbsp;to get started.</p><p><a href="https://cran.r-project.org/package=quanteda.textmodels">quanteda.textmodels</a>&nbsp;v0.9.1: Implements methods for scaling models and classifiers based on sparse matrix objects representing textual data. It includes implementations of the&nbsp;<a href="denied:doi:10.1017/S0003055403000698">Laver et al. (2003)</a>&nbsp;wordscores model, the&nbsp;<a href="denied:arxiv:1710.08963">Perry &amp; Benoit&rsquo;s (2017)</a>&nbsp;class affinity scaling model, and the&nbsp;<a href="denied:doi:10.1111/j.1540-5907.2008.00338.x">Slapin &amp; Proksch (2008)</a>&nbsp;wordfish model. See the&nbsp;<a href="https://cran.r-project.org/web/packages/quanteda.textmodels/vignettes/textmodel_performance.html">vignette</a>&nbsp;to get started.</p><p><a href="https://cran.r-project.org/package=SeqDetect">SeqDetect</a>&nbsp;v1.0.7: Implements the automaton model found in&nbsp;<a href="https://ieeexplore.ieee.org/document/8910574">Krleža, Vrdoljak &amp; Brčić (2019)</a>&nbsp;to detect and process sequences. See the&nbsp;<a href="https://cran.r-project.org/web/packages/SeqDetect/vignettes/SequentialDetector.pdf">vignette</a>&nbsp;for examples and theory.</p><p><a href="https://cran.r-project.org/package=studyStrap">studyStrap</a>&nbsp;v1.0.0: Implements multi-Study Learning algorithms such as Merging, Study-Specific Ensembling (Trained-on-Observed-Studies Ensemble), the Study Strap, and the Covariate-Matched Study Strap. and offers over 20 similarity measures. See&nbsp;<a href="denied:doi:10.1101/856385">Kishida, et al. (2019)</a>&nbsp;for background and the&nbsp;<a href="https://cran.r-project.org/web/packages/studyStrap/vignettes/vignette.html">vignette</a>&nbsp;for how to use the package.</p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43254/quasr-quantification-and-annotation-of-short-reads-in-r</guid>
	<pubDate>Fri, 13 Aug 2021 07:44:05 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43254/quasr-quantification-and-annotation-of-short-reads-in-r</link>
	<title><![CDATA[QuasR: Quantification and annotation of short reads in R]]></title>
	<description><![CDATA[<p>The <em><a href="https://bioconductor.org/packages/3.14/QuasR">QuasR</a></em> package (short for <em>Qu</em>antify and <em>a</em>nnotate <em>s</em>hort reads in <em>R</em>) integrates the functionality of several <strong>R</strong> packages (such as <em><a href="https://bioconductor.org/packages/3.14/IRanges">IRanges</a></em> <span>(Lawrence et al. 2013)</span> and <em><a href="https://bioconductor.org/packages/3.14/Rsamtools">Rsamtools</a></em>) and external software (e.g.&nbsp;<code>bowtie</code>, through the <em><a href="https://bioconductor.org/packages/3.14/Rbowtie">Rbowtie</a></em> package, and <code>HISAT2</code>, through the <em><a href="https://bioconductor.org/packages/3.14/Rhisat2">Rhisat2</a></em> package). The package aims to cover the whole analysis workflow of typical high throughput sequencing experiments, starting from the raw sequence reads, over pre-processing and alignment, up to quantification. A single <strong>R</strong> script can contain all steps of a complete analysis, making it simple to document, reproduce or share the workflow containing all relevant details.</p><p>Address of the bookmark: <a href="https://www.bioconductor.org/packages/devel/bioc/vignettes/QuasR/inst/doc/QuasR.html" rel="nofollow">https://www.bioconductor.org/packages/devel/bioc/vignettes/QuasR/inst/doc/QuasR.html</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>

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