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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/37610?offset=30</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/27463/bpipe-a-tool-for-running-and-managing-bioinformatics-pipelines</guid>
	<pubDate>Sat, 21 May 2016 22:42:16 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/27463/bpipe-a-tool-for-running-and-managing-bioinformatics-pipelines</link>
	<title><![CDATA[Bpipe - a tool for running and managing bioinformatics pipelines]]></title>
	<description><![CDATA[<p>Bpipe provides a platform for running big bioinformatics jobs that consist of a series of processing stages - known as 'pipelines'.</p>
<ul>
<li>January 20th, 2016 - New! Bpipe 0.9.9 released!</li>
<li>Download <a href="http://download.bpipe.org/versions/bpipe-0.9.9.tar.gz">latest</a>, <a href="http://download.bpipe.org">all</a></li>
<li><a href="http://docs.bpipe.org">Documentation</a></li>
<li><a href="https://groups.google.com/forum/#%21forum/bpipe-discuss">Mailing List</a> (Google Group)</li>
</ul>
<p>Bpipe has been published in <a href="http://bioinformatics.oxfordjournals.org/content/early/2012/04/11/bioinformatics.bts167.abstract">Bioinformatics</a>! If you use Bpipe, please cite:</p>
<p><em>Sadedin S, Pope B &amp; Oshlack A, Bpipe: A Tool for Running and Managing Bioinformatics Pipelines, Bioinformatics</em></p><p>Address of the bookmark: <a href="http://docs.bpipe.org/" rel="nofollow">http://docs.bpipe.org/</a></p>]]></description>
	<dc:creator>Radha Agarkar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/28855/vcfr</guid>
	<pubDate>Fri, 19 Aug 2016 07:38:24 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/28855/vcfr</link>
	<title><![CDATA[vcfR]]></title>
	<description><![CDATA[<p><span>Most variant calling pipelines result in files containing large quantities of variant information. The&nbsp;</span><a href="http://samtools.github.io/hts-specs/" title="VCF format at hts-specs">variant call format (vcf)</a><span>&nbsp;is an increasingly popular format for this data. The format of these files and their content is discussed in the vignette &lsquo;vcf data.&rsquo; These files are typically intended to be post-processed (i.e., filtered) as an attempt to remove false positives or otherwise problematic sites. The R package vcfR provides tools to facilitate this filtering as well as to visualize the effects of choices made during this process.</span></p><p>Address of the bookmark: <a href="https://cran.r-project.org/web/packages/vcfR/vignettes/visualization_1.html" rel="nofollow">https://cran.r-project.org/web/packages/vcfR/vignettes/visualization_1.html</a></p>]]></description>
	<dc:creator>Archana Malhotra</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/29601/statistics-using-r-with-biological-examples</guid>
	<pubDate>Thu, 03 Nov 2016 04:55:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/29601/statistics-using-r-with-biological-examples</link>
	<title><![CDATA[Statistics Using R   with Biological Examples]]></title>
	<description><![CDATA[<p>This book is a manifestation of my desire to teach researchers in biology a bit more about statistics than an ordinary introductory course covers and to introduce the utilization of R as a tool for analyzing their data. My goal is to reach those with little or no training in higher level statistics so that they can do more of their own data analysis, communicate more with statisticians, and appreciate the great potential statistics has to offer as a tool to answer biological questions. </p><p>This is necessary in light of the increasing use of higher level statistics in biomedical research. I hope it accomplishes this mission and encourage its free distribution and use as a course text or supplement.</p><p>K Seefeld, May 2007</p>]]></description>
	<dc:creator>Neel</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/29601" length="4581031" type="application/pdf" />
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29656/statistics-and-probability</guid>
	<pubDate>Tue, 08 Nov 2016 07:34:25 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29656/statistics-and-probability</link>
	<title><![CDATA[Statistics and probability]]></title>
	<description><![CDATA[<h3><span>Topics</span></h3>
<div>
<div><a href="https://www.khanacademy.org/math/statistics-probability/displaying-describing-data">Displaying and describing data</a></div>
<div><a href="https://www.khanacademy.org/math/statistics-probability/modeling-distributions-of-data">Modeling distributions of data</a></div>
<div><a href="https://www.khanacademy.org/math/statistics-probability/describing-relationships-quantitative-data">Describing relationships in quantitative data</a></div>
<div><a href="https://www.khanacademy.org/math/statistics-probability/designing-studies">Designing studies</a></div>
<div><a href="https://www.khanacademy.org/math/statistics-probability/probability-library">Probability</a></div>
<div><a href="https://www.khanacademy.org/math/statistics-probability/random-variables-stats-library">Random variables</a></div>
<div><a href="https://www.khanacademy.org/math/statistics-probability/sampling-distributions-library">Sampling distributions</a></div>
<div><a href="https://www.khanacademy.org/math/statistics-probability/confidence-intervals-one-sample">Confidence intervals (one sample)</a></div>
<div><a href="https://www.khanacademy.org/math/statistics-probability/significance-tests-one-sample">Significance tests (one sample)</a></div>
<div><a href="https://www.khanacademy.org/math/statistics-probability/significance-tests-confidence-intervals-two-samples">Significance tests and confidence intervals (two samples)</a></div>
<div><a href="https://www.khanacademy.org/math/statistics-probability/inference-categorical-data-chi-square-tests">Inference for categorical data (chi-square tests)</a></div>
<div><a href="https://www.khanacademy.org/math/statistics-probability/advanced-regression-inference-transforming">Advanced regression (inference and tran</a></div>
</div><p>Address of the bookmark: <a href="https://www.khanacademy.org/math/statistics-probability" rel="nofollow">https://www.khanacademy.org/math/statistics-probability</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30897/finestructure-v2-globetrotter</guid>
	<pubDate>Mon, 13 Feb 2017 08:40:23 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30897/finestructure-v2-globetrotter</link>
	<title><![CDATA[fineSTRUCTURE v2 &amp; GLOBETROTTER]]></title>
	<description><![CDATA[<p>Software available at this site</p>
<div>
<ul>
<li><a href="https://people.maths.bris.ac.uk/%7Emadjl/finestructure/finestructure_info.html">FineSTRUCTURE version 2</a>, a pipeline for running ChromoPainter and FineSTRUCTURE for population inference. A GUI is available for interpretation. Download from the <a href="https://people.maths.bris.ac.uk/%7Emadjl/finestructure/finestructure.html">Downloads</a> page.</li>
<li><a href="https://people.maths.bris.ac.uk/%7Emadjl/finestructure/finestructureR.html">FineSTRUCTURE R scripts</a>, a facility for exploring the results when the GUI is unavailable.</li>
<li><a href="https://people.maths.bris.ac.uk/%7Emadjl/finestructure/globetrotter.html">GLOBETROTTER</a>, the admixture dating method based on ChromoPainter. Download from the <a href="https://people.maths.bris.ac.uk/%7Emadjl/finestructure/finestructure.html">Downloads</a> page.</li>
<li><a href="https://people.maths.bris.ac.uk/%7Emadjl/finestructure/admixture.html">AdmixturePainting</a>, A set of R tools to inmterpret the results of ADMIXTURE and STRUCTURE-like mixture models.</li>
<li><a href="https://people.maths.bris.ac.uk/%7Emadjl/finestructure/radpainter.html">RADpainter</a>, finestructure and ChromoPainter for RAD tag data used for non-model organisms.</li>
<li>Scripts to perform many types of conversion. Included in the main software download from the <a href="https://people.maths.bris.ac.uk/%7Emadjl/finestructure/finestructure.html">Downloads</a> page.</li>
</ul>
What this page is This page provides information about and downloads for <strong>methodology for Chromosome Painting</strong>. It is not a facility to analyse your genome. Sorry if you were misled by the punchy name!<br> About Chromosome Painting Painting is an efficient way of identifying important haplotype information from dense genotype data. It describes ancestry in an efficient way suitable for a range of further analyses, including population identification and admixture dating.</div><p>Address of the bookmark: <a href="http://paintmychromosomes.com/" rel="nofollow">http://paintmychromosomes.com/</a></p>]]></description>
	<dc:creator>Shruti Paniwala</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/1720/postdoctoral-associate-bioinformatics-at-duke-university-medical-center</guid>
  <pubDate>Sat, 10 Aug 2013 18:38:38 -0500</pubDate>
  <link></link>
  <title><![CDATA[Postdoctoral Associate - Bioinformatics  at Duke University Medical Center]]></title>
  <description><![CDATA[
<p>The Department of Biostatistics and Bioinformatics at Duke University Medical Center is seeking a Postdoctoral Associate for a one year appointment to work on several high-dimensional research projects. The specific goals of the project are to identify genes or molecular markers that are predictive of clinical outcomes in renal and prostate cancer.</p>

<p>Candidates must have: a PhD degree in statistics, biostatistics or bioinformatics, extensive experience in analyzing high-dimensional data (microarray, SNP, CNVs) and of validation approaches. In addition, experience in penalized regression methods, data base manipulation; and strong programming skills in order to conduct Monte Carlo studies and applications (R). Candidate must have excellent communication skills (verbal, written and presentation), a strong proficiency in Linux system.</p>

<p>This position is available immediately and will be filled as soon as possible. Appointment could be extended beyond the first year based on additional funding.</p>

<p>For more information about the Department of Biostatistics and Bioinformatics, please visit our website: http://www.biostat.duke.edu.</p>

<p>For more info: http://biostat.duke.edu/sites/biostat.duke.edu/files/Halabi%20-%20Postdoc%20Job%20Posting%202013%20updated.pdf</p>

<p>Duke University is an Equal Opportunity/Affirmative Action Employer.</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/2457/rdataminingcom-r-and-data-mining</guid>
	<pubDate>Thu, 15 Aug 2013 18:37:23 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/2457/rdataminingcom-r-and-data-mining</link>
	<title><![CDATA[Rdatamining.com : R and Data Mining]]></title>
	<description><![CDATA[<p>This website presents examples, documents and resources on data mining with R. <br>Documents on using R for data mining are available to download for non-commercial personal use, including&nbsp;R Reference card for Data Mining, R and Data Mining: Examples and Case Studies and Time Series Analysis and Mining with R.</p><p>Address of the bookmark: <a href="http://www.rdatamining.com/" rel="nofollow">http://www.rdatamining.com/</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/41905/research-associate-bioinformatics-in-iisc-recruitment-2020</guid>
  <pubDate>Tue, 23 Jun 2020 21:53:34 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research Associate Bioinformatics in IISc Recruitment 2020]]></title>
  <description><![CDATA[
<p>Research Associate Bioinformatics in IISc Recruitment 2020</p>

<p>Essential Qualifications: Ph.D. (Bioinformatics/ Biophysics/ Biotechnology or any other stream of biological/ physical sciences) with a minimum of two publications in reputed peer reviewed journals in the area of structural bioinformatics or biophysics or biomolecular modeling/ simulation.</p>

<p>Job description: Development of bioinformatics tools and algorithms/software for structure based analysis of biomolecular systems. Programmatic access to major biomolecular databases using APIs Knowledge based prediction and analysis of biomolecular structure, function and interactions. Docking/simulations for inhibitor design.</p>

<p>Desirable Qualifications (Research Associate/s): i)  Strong computer programming skills (in Python/PERL/PHP or C++ or object oriented database management systems like MySQL etc or scripting languages under LINUX/UNIX environment). </p>

<p>ii) Extensive experience in computational analysis of biomolecular structure/interactions and usage of advanced biomolecular simulation softwares. iii) Adequate knowledge of major databases, webservers and softwares in the area of biomolecular structure/function and drug design. iv)  Familiarity with Parallel Programming environments and experience in usage of high-end HPC clusters.</p>

<p>The candidates must highlight their experience in above mentioned fields/topics in their CV. Initial appointment will be for a period of 1 year, subject to extension after review of performance.</p>

<p>Emoluments: As per DST, GOI norms and commensurate with experience.</p>

<p>More at https://www.iisc.ac.in/positions-open/</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22891/17-marie-curie-phd-position-available-immediately</guid>
  <pubDate>Tue, 23 Jun 2015 06:52:06 -0500</pubDate>
  <link></link>
  <title><![CDATA[17 Marie Curie PhD position available immediately]]></title>
  <description><![CDATA[
<p>Kindly look into following webpage:<br />http://medhealth.leeds.ac.uk/info/1450/scholarships/1795/marie_curie_phd_training_network</p>

<p>The closing date for application will be 26 June 2015.</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/35868/simpson-lab</guid>
  <pubDate>Tue, 06 Mar 2018 08:59:09 -0600</pubDate>
  <link></link>
  <title><![CDATA[Simpson Lab]]></title>
  <description><![CDATA[
<p>We are the Statistical Bioinformatics group in the Institute for Adaptive and Neural Computation in the School of Informatics at the University of Edinburgh. The group is led by Dr. Ian Simpson who is a Lecturer in Biological Informatics in the School of Informatics at Edinburgh University. Details to follow....</p>

<p>http://statbio.github.io</p>
]]></description>
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