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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/27070?offset=890</link>
	<atom:link href="https://bioinformaticsonline.com/related/27070?offset=890" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/37586/julia-programming-language-a-python-and-r-rival</guid>
	<pubDate>Sat, 25 Aug 2018 04:46:39 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/37586/julia-programming-language-a-python-and-r-rival</link>
	<title><![CDATA[Julia Programming Language, a Python and R rival]]></title>
	<description><![CDATA[<p>Big data has grown to become one of the most lucrative fields. In fact, data scientists are some of the most sought people. They are usually hired to analyze, control and parse large chunks of data. Implementing these actions using traditional techniques is not a walk in the park. This is why most data scientists prefer using programming languages such as R and Python. However, there is one more programming language that can do the job. That is Julia programming language.</p><p>What Is Julia Language?</p><p>Julia is a programming language that came into the limelight in 2012. It is a general-purpose programming language that was designed for solving scientific computations. Julia was meant to be an alternative to Python, R and other programming languages that were mainly used for manipulating data. This is because it has numerous features that can minimize the complexities of numerical computations.&nbsp;</p><p>Julia optimizes on the best features of Python and R while at the same time overlooks their weaknesses. This explains why it is viewed as an alternative to these programming languages. For instance, it utilizes the readability and simplicity of Python then performs faster.</p><p>Julia is the most preferred programming language for data scientists and mathematicians. This is because its core features are similar to the ones that are used on most data software. Also, the language is ideal for these two subjects because its syntax is similar to the standard mathematical formulas.</p><p>Key Features Of Julia Language<br />Uses JIT Compilation<br />Parallelism<br />Dynamic Typing<br />Simple Syntax<br />Allows Metaprogramming<br />Accessible to Libraries<br />-1-Array Indexing</p><p>Julia Vs Python And R Programming Languages<br />1. Speed<br />Julia is faster than both Python and R. This is a very critical aspect that is given special attention in the big data programming. The high speed of Julia is because of JIT compilers. You will need to install external libraries on Python to achieve similar speed.</p><p>2. Syntax<br />Julia has a math-friendly syntax. The syntax of this programming language is similar to the mathematical formulas hence can be used to perform mathematical and scientific computations. This syntax makes it easier to learn than Python.</p><p>3. Parallelism<br />Although both Python and R use parallelism, Julia uses a top-level parallelism. Julia allows the processor to perform to the optimum level than what Python and R can achieve.</p><p>4. Versatility<br />Julia programming language is more versatile than Python and R. It allows a programmer to move from different codes and functions with ease.</p><p>The only area that Python and R are superior to Julia is in terms of community. Given that Julia is a new programming language, it has a small community as compared to others which have been around for years.</p><p>In overall Julia programming language is a better alternative that you can use to handle Big data projects. Despite having a small community, it is one of those programming languages that you can easily learn.</p>]]></description>
	<dc:creator>Radha Agarkar</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/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>
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	<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>
</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/news/view/14186/pybedtools</guid>
	<pubDate>Wed, 20 Aug 2014 01:03:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/14186/pybedtools</link>
	<title><![CDATA[pybedtools]]></title>
	<description><![CDATA[<p>pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs (https://github.com/arq5x/bedtools), which are widely used for genomic interval manipulation or "genome algebra". pybedtools extends BEDTools by offering feature-level manipulations from with Python. See full online documentation, including installation instructions, at http://pythonhosted.org/pybedtools/.</p><p>More at http://pythonhosted.org/pybedtools/</p><p>A powerful toolset for genome arithmetic.http://code.google.com/p/bedtools/</p>]]></description>
	<dc:creator>Shruti Paniwala</dc:creator>
</item>
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	<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>
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	<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>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44414/reconplot-an-r-package-for-the-visualization-and-interpretation-of-genomic-rearrangements</guid>
	<pubDate>Thu, 14 Dec 2023 12:33:19 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44414/reconplot-an-r-package-for-the-visualization-and-interpretation-of-genomic-rearrangements</link>
	<title><![CDATA[ReConPlot: an R package for the visualization and interpretation of genomic rearrangements]]></title>
	<description><![CDATA[<p>ReConPlot (REarrangement and COpy Number PLOT), an R package that provides functionalities for the joint visualization of SCNAs and SVs across one or multiple chromosomes. ReConPlot is based on the popular ggplot2 package, thus allowing customization of plots and the generation of publication-quality figures with minimal effort.</p><p>Address of the bookmark: <a href="https://academic.oup.com/bioinformatics/article/39/12/btad719/7460198?login=false" rel="nofollow">https://academic.oup.com/bioinformatics/article/39/12/btad719/7460198?login=false</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>

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