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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/39884?offset=0</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39898/itis-the-integrated-taxonomic-information-system</guid>
	<pubDate>Fri, 30 Aug 2019 23:07:15 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39898/itis-the-integrated-taxonomic-information-system</link>
	<title><![CDATA[ITIS: the Integrated Taxonomic Information System!]]></title>
	<description><![CDATA[<p><span>ITIS, the Integrated Taxonomic Information System! Here you will find authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world. We are a&nbsp;</span><a href="https://www.itis.gov/organ.html">partnership</a><span>&nbsp;of U.S.,&nbsp;</span><a href="http://www.cbif.gc.ca/eng/home/?id=1370403266262" target="_blank">Canadian</a><span>, and&nbsp;</span><a href="http://www.conabio.gob.mx/" target="_blank">Mexican</a><span>&nbsp;agencies (</span><a href="http://www.cbif.gc.ca/eng/integrated-taxonomic-information-system-itis/?id=1381347793621" target="_blank">ITIS-North America</a><span>); other organizations; and taxonomic specialists. ITIS is also a partner of&nbsp;</span><a href="http://www.sp2000.org/" target="_blank">Species 2000</a><span>&nbsp;and the&nbsp;</span><a href="http://www.gbif.org/" target="_blank">Global Biodiversity Information Facility (GBIF)</a><span>. The ITIS and Species 2000&nbsp;</span><a href="http://www.catalogueoflife.org/annual-checklist/" target="_blank">Catalogue of Life (CoL)</a><span>partnership is proud to provide the taxonomic backbone to the&nbsp;</span><a href="http://www.eol.org/" target="_blank">Encyclopedia of Life (EOL)</a><span>.&nbsp;</span></p>
<p><span><a href="https://www.itis.gov/pdf/twb_ug.pdf">https://www.itis.gov/pdf/twb_ug.pdf</a></span></p><p>Address of the bookmark: <a href="https://www.itis.gov/" rel="nofollow">https://www.itis.gov/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/27070/venn-diagrams-on-r-studio</guid>
	<pubDate>Mon, 25 Apr 2016 16:22:28 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/27070/venn-diagrams-on-r-studio</link>
	<title><![CDATA[Venn Diagrams on R Studio]]></title>
	<description><![CDATA[<h3>First step: Install &amp; load &ldquo;VennDiagram&rdquo; package.</h3>
<pre><code><span># install.packages('VennDiagram')</span>
<span>library</span><span>(</span><span>VennDiagram</span><span>)</span>
</code></pre>
<h3>Second step: Load data</h3>
<p>Add filepath if &ldquo;catdoge.csv&rdquo; is not in working-directory.</p>
<pre><code><span>d</span> <span>&lt;-</span> <span>read.csv</span><span>(</span><span>"catdoge.csv"</span><span>)</span></code><br><br></pre><p>Address of the bookmark: <a href="http://rstudio-pubs-static.s3.amazonaws.com/13301_6641d73cfac741a59c0a851feb99e98b.html" rel="nofollow">http://rstudio-pubs-static.s3.amazonaws.com/13301_6641d73cfac741a59c0a851feb99e98b.html</a></p>]]></description>
	<dc:creator>Jitendra Prajapati</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/29624/information-officer-at-iiar-gujarat</guid>
  <pubDate>Fri, 04 Nov 2016 05:19:13 -0500</pubDate>
  <link></link>
  <title><![CDATA[Information Officer at IIAR, Gujarat]]></title>
  <description><![CDATA[
<p>Walk in interview at 10.30 am on Nov 11th, 2016 for the following position at Distributed Information Sub-Centre (DISC) established by Dept. Of Biotechnology, Govt. of India at Indian Institute of Advanced Research, Gandhinagar, Gujarat</p>

<p>Position (scale), qualifications and experience</p>

<p>1. Information Officer (Rs 8000-275-13500): one post <br />Qualifications and experience: MCA, Post-Graduate in any field of biosciences, bioinformatics with at least two years of experience in working in a bioinformatics setup and good knowledge of linux operating system and computer networking.</p>

<p>General terms and conditions: <br />1. The above engagements is presently till March 31st, 2017. However on extension of project grant and satisfactory performance of the candidate, your services can be extended beyond March 31st, 2017 based on the terms and conditions of extension of project grant.</p>

<p>2. It is not an appointment with the institute and will not confer any right to the incumbent to any claim implicit or explicit on any position.</p>

<p>3.No TA/DA will be paid for attending the interview. Outstation candidates have to make their own arrangement for their stay.</p>

<p>4.Candidates, appearing in the walk-in interview are requested to bring the hard copy of application addressed to Dr. Anju Pappachan with latest photograph, CV mentioning qualifications, work experience and name of two referees and one page write up as to why you would like to join the project.</p>

<p>Address: <br />Dr. Anju Pappachan <br />Indian Institute of Advanced Research (IIAR), <br />University  and Institute of Advanced Research, <br />The Puri Foundation for Education in India, <br />Koba Institutional Area, <br />Gandhinagar- 382 007, Gujarat, India. Contact no. 079-30514152 <br />e-mail- anju@iiar.res.in</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38749/clipcrop-a-tool-for-detecting-structural-variations-with-single-base-resolution-using-soft-clipping-information</guid>
	<pubDate>Sun, 20 Jan 2019 06:34:36 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38749/clipcrop-a-tool-for-detecting-structural-variations-with-single-base-resolution-using-soft-clipping-information</link>
	<title><![CDATA[ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information]]></title>
	<description><![CDATA[<p><span>ClipCrop for detecting SVs with single-base resolution using soft-clipping information. A soft-clipped sequence is an unmatched fragment in a partially mapped read. To assess the performance of ClipCrop with other SV-detecting tools, we generated various patterns of simulation data &ndash; SV lengths, read lengths, and the depth of coverage of short reads &ndash; with insertions, deletions, tandem duplications, inversions and single nucleotide alterations in a human chromosome.&nbsp;</span></p><p>Address of the bookmark: <a href="https://github.com/shinout/clipcrop" rel="nofollow">https://github.com/shinout/clipcrop</a></p>]]></description>
	<dc:creator>BioJoker</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/924/try-r-online</guid>
	<pubDate>Tue, 16 Jul 2013 06:15:11 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/924/try-r-online</link>
	<title><![CDATA[Try R Online]]></title>
	<description><![CDATA[<p>One of the best R tutorial website, which provide an online interative interface to try and learn R language without any hassle.</p><p>Link @ http://tryr.codeschool.com/</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/3046/r-and-bioconductor-tutorial</guid>
	<pubDate>Fri, 23 Aug 2013 08:23:59 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/3046/r-and-bioconductor-tutorial</link>
	<title><![CDATA[R and Bioconductor Tutorial]]></title>
	<description><![CDATA[<p>This tutorial is intended to introduce users quickly to the basics of R, focusing on a few common tasks that &nbsp;biologists need to perform &nbsp;some basic analysis: &nbsp;load a table, plot some graphs, and perform some basic statistics. More extensive tutorials can be found on the project website and via bioconductor (not covered here).</p>
<p>You can add more tutorial links in comments if found new pages.</p><p>Address of the bookmark: <a href="http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual" rel="nofollow">http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual</a></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/11030/r-programming-and-jobs-website</guid>
	<pubDate>Sun, 25 May 2014 14:43:57 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/11030/r-programming-and-jobs-website</link>
	<title><![CDATA[R programming and Jobs website]]></title>
	<description><![CDATA[<p>Welcome to the R Jobs section of ProgrammingR.com. If your organization has an R employment opportunity that you would like to have posted here, submit it via the <a href="http://www.programmingr.com/contact" title="contact page">contact page</a>. Prospective employees: use the contact information provided in the position listing to apply or contact the hiring organization.</p><p>Address of the bookmark: <a href="http://www.programmingr.com/category/stype/r-job-listings/" rel="nofollow">http://www.programmingr.com/category/stype/r-job-listings/</a></p>]]></description>
	<dc:creator>Pragati Singh</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/19087/dcgor</guid>
	<pubDate>Sat, 08 Nov 2014 14:54:28 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/19087/dcgor</link>
	<title><![CDATA[dcGOR]]></title>
	<description><![CDATA[<p>An R package for analysing ontologies and protein domain annotations has been published in PLoS Computational Biology (http://dx.doi.org/10.1371/journal.pcbi.1003929). The package is distributed as part of CRAN (http://cran.r-project.org/package=dcGOR), and also at GitHub for version control.<br /><br />The dedicated website is available in http://supfam.org/dcGOR, from which several demos are also provided:<br /><br />1. Analysing SCOP domains: http://supfam.org/dcGOR/demo-Fang.html<br /><br />2. Analysing Pfam domains: http://supfam.org/dcGOR/demo-Basu.html<br /><br />3. Analysing InterPro domains: http://supfam.org/dcGOR/demo-Customisation.html<br /><br />&nbsp;</p>]]></description>
	<dc:creator>Martin Jones</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/21312/r-for-microsoft-excel</guid>
	<pubDate>Wed, 18 Feb 2015 00:43:27 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/21312/r-for-microsoft-excel</link>
	<title><![CDATA[R for Microsoft Excel]]></title>
	<description><![CDATA[<div><p>If you currently use a spreadsheet like Microsoft Excel for data analysis, you might be interested in taking a look at this <a href="https://districtdatalabs.silvrback.com/intro-to-r-for-microsoft-excel-users" target="_blank">tutorial on how to transition from Excel to R</a>&nbsp;by Tony Ojeda. The tutorial explains how to use R functions in place of Excel formulas, including tools like =AVERAGE and =VLOOKUP. For the most part, it uses modern R packages to keep the R code clear and concise.</p><p>You'll likely still be using Excel as a data source, though, so you'll also want to check out this <a href="http://www.milanor.net/blog/?p=779" target="_blank">guide to importing data from Excel to R</a> from MilanoR.</p></div><p>Reference http://www.r-bloggers.com/an-r-tutorial-for-microsoft-excel-users/</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/21444/a-guide-for-complete-r-beginners-installing-r-packages</guid>
	<pubDate>Tue, 24 Feb 2015 20:23:34 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/21444/a-guide-for-complete-r-beginners-installing-r-packages</link>
	<title><![CDATA[A guide for complete R beginners :- Installing R packages]]></title>
	<description><![CDATA[<p>Part of the reason R has become so popular is the vast array of packages available at the <a href="http://cran.r-project.org/" target="_blank">cran</a> and <a href="http://www.bioconductor.org/" target="_blank">bioconductor</a> repositories. In the last few years, the number of packages has grown <a href="http://blog.revolutionanalytics.com/2010/09/what-can-other-languages-learn-from-r.html" target="_blank">exponentially</a>!</p><p>This is a short post giving steps on how to actually install R packages. Let&rsquo;s suppose you want to install the <a href="http://had.co.nz/ggplot2/" target="_blank">ggplot2</a> package. Well nothing could be easier. We just fire up an R shell and type:<br /><code><br />&gt; install.packages("ggplot2")</code></p><p>In theory the package should just install, however:</p><ul>
<li>if you are using Linux and don&rsquo;t have root access, this command won&rsquo;t work.</li>
<li>you will be asked to select your local mirror, i.e. which server should you use to download the package.</li>
</ul><h4>Installing packages without root access</h4><p>First, you need to designate a directory where you will store the downloaded packages. On my machine, I use the directory <code>/data/Rpackages/</code> After creating a package directory, to install a package we use the command:<br /><code><br />&gt; install.packages("ggplot2"</code><code>, lib="/data/Rpackages/")<br />&gt; library(ggplot2, lib.loc="/data/Rpackages/")<br /></code></p><p>It&rsquo;s a bit of a pain having to type <code>/data/Rpackages/</code> all the time. To avoid this burden,&nbsp; we create a file <code>.Renviron</code> in our home area, and add the line <code>R_LIBS=/data/Rpackages/</code> to it. This means that whenever you start R, the directory <code>/data/Rpackages/</code> is added to the list of places to look for R packages and so:</p><p><code>&gt; install.packages("ggplot2"</code><code>)<br />&gt; library(ggplot2)</code></p><p>just works!</p><h4>Setting the repository</h4><p>Every time you install a R package, you are asked which repository R should use. To set the repository and avoid having to specify this at every package install, simply:</p><ul>
<li>create a file <code>.Rprofile</code> in your home area.</li>
<li>Add the following piece of code to it:</li>
</ul><p><code><br />cat(".Rprofile: Setting UK repositoryn")<br />r = getOption("repos") # hard code the UK repo for CRAN<br />r["CRAN"] = "http://cran.uk.r-project.org"<br />options(repos = r)<br />rm(r)<br /></code></p><p>I found this tip in a stackoverflow <a href="http://stackoverflow.com/questions/1189759/expert-r-users-whats-in-your-rprofile/1189826#1189826" target="_blank">answer </a>.</p>]]></description>
	<dc:creator>Archana Malhotra</dc:creator>
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