<?xml version='1.0'?><rss version="2.0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:georss="http://www.georss.org/georss" xmlns:atom="http://www.w3.org/2005/Atom" >
<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/41991?offset=940</link>
	<atom:link href="https://bioinformaticsonline.com/related/41991?offset=940" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36755/minialign-fast-and-accurate-alignment-tool-for-pacbio-and-nanopore-long-reads</guid>
	<pubDate>Thu, 24 May 2018 08:33:26 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36755/minialign-fast-and-accurate-alignment-tool-for-pacbio-and-nanopore-long-reads</link>
	<title><![CDATA[minialign: fast and accurate alignment tool for PacBio and Nanopore long reads]]></title>
	<description><![CDATA[Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.<p>Address of the bookmark: <a href="https://github.com/ocxtal/minialign" rel="nofollow">https://github.com/ocxtal/minialign</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/22017/binc-2015</guid>
	<pubDate>Sat, 11 Apr 2015 20:35:27 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/22017/binc-2015</link>
	<title><![CDATA[BINC 2015 !!!]]></title>
	<description><![CDATA[<p>Pondicherry University,Puducherry,on behalf of Department of Biotechnology, Government of India, will conduct the BINC examination in2015. The objective of this examination is to certify bioinformatics professionals, trained formally as well as self-trained.Registration will open from March 9,2015 to April 30,2015. Pondicherry University, Puducherry has been identified as a nodal agency by the Department of Biotechnology, Govt. of India to coordinate this examination along with nine centres namely, Pune University, Pune; Anna University, Chennai; Calcutta University, Kolkata; Institute of Bioinformatics &amp; Applied Biotechnology, Bangalore; North-Eastern Hill University, Shillong, University of Hyderabad, Hyderabad; University of Kerala, Thiruvananthapuram; Jawaharlal Nehru University, New Delhi and Assam Agricultural University, Guwahati. In the BINC 2013 examination,17 candidates were certified. DBT has agreed to fund Research fellowships for all the BINC qualified Indian nationals to pursue Ph.D. in Indian Institutes/Universities. Note that the candidate must possess a postgraduate degree(or equivalent) &amp; meet the criteria of the institutes/universities in order to avail research fellowship. In addition, cash prize of Rs. 10,000/- will be awarded to the top 10 BINC qualifiers.</p><p>More at http://www.binc.co.in/College/Index_New.aspx</p><p>BINC notification http://www.binc.co.in/PdfDocuments/Notification.pdf</p><p>Few dates to remember:</p><p>Starting of online submission of application: March 9, 2015<br />Last date for submission of application: April 30,2015<br />Examination consists of two parts:<br />Part I (Paper I) : June 7, 2015 (10 AM-12 PM)<br />Part II ( Paper II &amp; III) :June 28, 2015 (9 AM-12 PM &amp; 2 PM-4 PM)</p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36905/d-genies-a-tool-for-dotplot-large-genomes-in-an-interactive-efficient-and-simple-way</guid>
	<pubDate>Mon, 11 Jun 2018 09:41:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36905/d-genies-a-tool-for-dotplot-large-genomes-in-an-interactive-efficient-and-simple-way</link>
	<title><![CDATA[D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way]]></title>
	<description><![CDATA[D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation.

We use minimap version 2 to align the two genomes. Then, the PAF file is parsed and plotted into an interactive plot written with d3.js library.

D-Genies also allows to display dot plots from other aligners by uploading their PAF or MAF alignment file.

http://dgenies.toulouse.inra.fr/<p>Address of the bookmark: <a href="http://dgenies.toulouse.inra.fr/" rel="nofollow">http://dgenies.toulouse.inra.fr/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22040/karpagam-university-coimbatore-of-sr-prof-prof-associate-and-assistant-professors-karpagam-university-coimbatore-coimbatore-tamil-nadu</guid>
  <pubDate>Thu, 16 Apr 2015 00:30:45 -0500</pubDate>
  <link></link>
  <title><![CDATA[Karpagam University, Coimbatore, of Sr. Prof, Prof, Associate and Assistant Professors Karpagam University, Coimbatore - Coimbatore, Tamil Nadu]]></title>
  <description><![CDATA[
<p>Karpagam University, Coimbatore, Recruitment of Sr. Prof, Prof, Associate and Assistant Professors</p>

<p>Name of the College: Karpagam University, Coimbatore</p>

<p>Date of official publication: 15th April 2015</p>

<p>The newspaper wherein this job advertised: The Hindu Newspaper</p>

<p>Name of the posts: Senior Professors, Professors, Associate Professors and Assistant Professors</p>

<p>Departments:<br />Bioinformatics<br />Biotechnology<br />Qualifications/Eligibility: The candidates should have qualifications as M.E/M.Tech/M.A/M.Com/MBA/M.Sc/M.Phil/NET/SLET/Ph.D</p>

<p>Job Location: Coimbatore, TN</p>

<p>Salary: As per college norms</p>

<p>How to apply: Interested and eligible candidates are requested to apply online at http://www.karpagamuniversity.edu.in/career</p>

<p>Last date: As soon as possible from 15th April 2015</p>

<p>Reference: The Hindu Newspaper dated 15-04-2015, Coimbatore edition on 14th page</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37496/gsearch-a-fast-and-flexible-general-search-tool-for-whole-genome-sequencing</guid>
	<pubDate>Mon, 06 Aug 2018 17:19:15 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37496/gsearch-a-fast-and-flexible-general-search-tool-for-whole-genome-sequencing</link>
	<title><![CDATA[gSearch: a fast and flexible general search tool for whole-genome sequencing]]></title>
	<description><![CDATA[<p><span>gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a multi-threaded manner.&nbsp;</span></p><p>Address of the bookmark: <a href="http://ml.ssu.ac.kr/gSearch/index.html" rel="nofollow">http://ml.ssu.ac.kr/gSearch/index.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/22053/binc-sample-question-paper</guid>
	<pubDate>Thu, 16 Apr 2015 09:16:18 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/22053/binc-sample-question-paper</link>
	<title><![CDATA[BINC Sample Question Paper !!!]]></title>
	<description><![CDATA[<p>BINC sample question paper. Wish you all the best for BINC examination.</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/22053" length="4041" type="text/plain" />
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37576/lrcstats-a-tool-for-evaluating-long-reads-correction-methods</guid>
	<pubDate>Wed, 22 Aug 2018 11:05:04 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37576/lrcstats-a-tool-for-evaluating-long-reads-correction-methods</link>
	<title><![CDATA[LRCstats: a tool for evaluating long reads correction methods]]></title>
	<description><![CDATA[<p><span>LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation sequencing technology, as the name suggests, are longer in length than reads produced by next generation sequencing technologies, such as those produced by Illumina. However, long reads are plagued by high error rates, which can cause issues in downstream analysis. Long read correction algorithms reduce the error rate of long reads either through self-correcting methods or using accurate, short reads outputted by next generation sequencing technologies to correct long reads.</span></p><p>Address of the bookmark: <a href="https://github.com/cchauve/lrcstats" rel="nofollow">https://github.com/cchauve/lrcstats</a></p>]]></description>
	<dc:creator>Aaryan Lokwani</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/22133/r-320-is-released</guid>
	<pubDate>Sat, 18 Apr 2015 05:06:44 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/22133/r-320-is-released</link>
	<title><![CDATA[R 3.2.0 is released]]></title>
	<description><![CDATA[<p>R 3.2.0 (codename &ldquo;Full of Ingredients&rdquo;)&nbsp;was <a href="http://r.789695.n4.nabble.com/R-3-2-0-is-released-td4705933.html" target="_blank">released yesterday</a>.&nbsp;You can get the latest binaries version <strong><a href="http://cran.rstudio.com/" target="_blank">from here</a>.</strong>&nbsp;(or the .tar.gz&nbsp;<strong>source</strong> code from <a href="http://cran.r-project.org/src/base/R-3/R-3.2.0.tar.gz" target="_blank">here</a>).&nbsp;The full list of new features and bug fixes is provided below.</p><h3>Upgrading to R 3.2.0 on Windows</h3><p>If you are using <strong>Windows&nbsp;</strong>you can easily upgrade to the latest version of R using <a href="http://cran.r-project.org/web/packages/installr/" target="_blank">the installr package</a>. Simply run the following code:</p><div><table>
<tbody>
<tr id="p612572">
<td id="p61257code2">
<pre><span style="color: #228b22;"># installing/loading the latest installr package:</span>
<span style="color: #0000ff; font-weight: bold;">install.<span>packages</span></span><span style="color: #080;">(</span><span style="color: #ff0000;">"installr"</span><span style="color: #080;">)</span><span style="color: #080;">;</span> <span style="color: #0000ff; font-weight: bold;">library</span><span style="color: #080;">(</span>installr<span style="color: #080;">)</span> <span style="color: #228b22;">#load / install+load installr</span>
&nbsp;
updateR<span style="color: #080;">(</span><span style="color: #080;">)</span> <span style="color: #228b22;"># updating R.</span></pre>
</td>
</tr>
</tbody>
</table></div><p><span>Running &ldquo;updateR()&rdquo; will detect if there is a new R version available, and if so it will download+install it (etc.).</span></p><p><span><strong>If you are an R blogger yourself</strong> you are invited to <a href="http://www.r-bloggers.com/add-your-blog/">add your own R content feed to this site</a> (<strong>Non-English</strong> R bloggers should add themselves- <a href="http://www.r-bloggers.com/lang/add-your-blog">here</a>)</span></p><h4>NEW FEATURES</h4><ul>
<li><code>anyNA()</code> gains a <code>recursive</code> argument.</li>
<li>When <code>x</code> is missing and <code>names</code> is not false (including the default value), <code>Sys.getenv(x, names)</code> returns an object of class <code>"Dlist"</code> and hence prints tidily.</li>
<li>(Windows.) <code>shell()</code> no longer consults the environment variable <span>SHELL</span>: too many systems have been encountered where it was set incorrectly (usually to a path where software was compiled, not where it was installed). <span>R_SHELL</span>, the preferred way to select a non-default shell, can be used instead.</li>
<li>Some unusual arguments to <code>embedFonts()</code> can now be specified as character vectors, and the defaults have been changed accordingly.</li>
<li>Functions in the <code>Summary</code> group duplicate less. (<a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15798" target="_blank">PR#15798</a>)</li>
<li>(Unix-alikes.) <code>system(cmd, input = )</code> now uses &lsquo;shell-execution-environment&rsquo; redirection, which will be more natural if <code>cmd</code> is not a single command (but requires a POSIX-compliant shell). (Wish of <a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15508" target="_blank">PR#15508</a>)</li>
<li><code>read.fwf()</code> and <code>read.DIF()</code> gain a <code>fileEncoding</code> argument, for convenience.</li>
<li>Graphics devices can add attributes to their description in <code>.Device</code> and <code>.Devices</code>. Several of those included with <strong>R</strong> use a <code>"filepath"</code> attribute.</li>
<li><code>pmatch()</code> uses hashing in more cases and so is faster at the expense of using more memory. (<a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15697" target="_blank">PR#15697</a>)</li>
<li><code>pairs()</code> gains new arguments to select sets of variables to be plotted against each other.</li>
<li><code>file.info(, extra_cols = FALSE)</code> allows a minimal set of columns to be computed on Unix-alikes: on some systems without properly-configured caching this can be significantly faster with large file lists.</li>
<li>New function <code>dir.exists()</code> in package <span>base</span> to test efficiently whether one or more paths exist and are directories.</li>
<li><code>dput()</code> and friends gain new controls <span>hexNumeric</span> and <span>digits17</span> which output double and complex quantities as, respectively, binary fractions (exactly, see <code>sprintf("%a")</code>) and as decimals with up to 17 significant digits.</li>
<li><code>save()</code>, <code>saveRDS()</code> and <code>serialize()</code> now support <code>ascii = NA</code> which writes ASCII files using <code>sprintf("%a")</code> for double/complex quantities. This is read-compatible with <code>ascii = TRUE</code> but avoids binary-&gt;decimal-&gt;binary conversions with potential loss of precision. Unfortunately the Windows C runtime&rsquo;s lack of C99 compliance means that the format cannot be read correctly there in <strong>R</strong> before 3.1.2.</li>
<li>The default for <code>formatC(decimal.mark =)</code> has been changed to be <code>getOption("OutDec")</code>; this makes it more consistent with <code>format()</code> and suitable for use in print methods, e.g. those for classes <code>"density"</code>, <code>"ecdf"</code>, <code>"stepfun"</code> and <code>"summary.lm"</code>.
<p><code>getOption("OutDec")</code> is now consulted by the print method for class <code>"kmeans"</code>, by <code>cut()</code>, <code>dendrogram()</code>, <code>plot.ts()</code> and <code>quantile()</code> when constructing labels and for the report from<code>legend(trace = TRUE)</code>.</p>
<p>(In part, wish of <a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15819" target="_blank">PR#15819</a>.)</p>
</li>
<li><code>printNum()</code> and hence <code>format()</code> and <code>formatC()</code> give a warning if <code>big.mark</code> and <code>decimal.mark</code> are set to the same value (period and comma are not uncommonly used for each, and this is a check that conventions have not got mixed).</li>
<li><code>merge()</code> can create a result which uses long vectors on 64-bit platforms.</li>
<li><code>dget()</code> gains a new argument <code>keep.source</code> which defaults to <code>FALSE</code> for speed (<code>dput()</code> and <code>dget()</code> are most often used for data objects where this can make <code>dget()</code> many times faster).</li>
<li>Packages may now use a file of common macro definitions in their help files, and may import definitions from other packages.</li>
<li>A number of macros have been added in the new &lsquo;<span>share/Rd</span>&rsquo; directory for use in package overview help pages, and <code>promptPackage()</code> now makes use of them.</li>
<li><code>tools::parse_Rd()</code> gains a new <code>permissive</code> argument which converts unrecognized macros into text. This is used by <code>utils:::format.bibentry</code> to allow LaTeX markup to be ignored.</li>
<li><code>options(OutDec =)</code> can now specify a multi-byte character, e.g., <code>options(OutDec = "u00b7")</code> in a UTF-8 locale.</li>
<li><code>is.recursive(x)</code> is no longer true when <code>x</code> is an external pointer, a weak reference or byte code; the first enables <code>all.equal(x, x)</code> when <code>x .</code></li>
<li><code>ls()</code> (aka <code>objects()</code>) and <code>as.list.environment()</code> gain a new argument <code>sorted</code>.</li>
<li>The <code>"source"</code> attribute (which has not been added to functions by <strong>R</strong> since before <strong>R</strong> version 2.14.0) is no longer treated as special.</li>
<li>Function <code>returnValue()</code> has been added to give <code>on.exit()</code> code access to a function&rsquo;s return value for debugging purposes.</li>
<li><code>crossprod(x, y)</code> allows more matrix coercions when <code>x</code> or <code>y</code> are vectors, now equalling <code>t(x) %*% y</code> in these cases (also reported by Radford Neal). Similarly, <code>tcrossprod(x,y)</code> and <code>%*%</code> work in more cases with vector arguments.</li>
<li>Utility function <code>dynGet()</code> useful for detecting cycles, aka infinite recursions.</li>
<li>The byte-code compiler and interpreter include new instructions that allow many scalar subsetting and assignment and scalar arithmetic operations to be handled more efficiently. This can result in significant performance improvements in scalar numerical code.</li>
<li><code>apply(m, 2, identity)</code> is now the same as the matrix <code>m</code> when it has <em>named</em> row names.</li>
<li>A new function <code>debuggingState()</code> has been added, allowing to temporarily turn off debugging.</li>
<li><code>example()</code> gets a new optional argument <code>run.donttest</code> and <code>tools::Rd2ex()</code> a corresponding <code>commentDonttest</code>, with a default such that <code>example(..)</code> in help examples will run <code>donttest</code> code only if used interactively (a change in behaviour).</li>
<li><code>rbind.data.frame()</code> gains an optional argument <code>make.row.names</code>, for potential speedup.</li>
<li>New function <code>extSoftVersion()</code> to report on the versions of third-party software in use in this session. Currently reports versions of <code>zlib</code>, <code>bzlib</code>, the <code>liblzma</code> from <code>xz</code>, PCRE, ICU, TRE and the <code>iconv</code> implementation.
<p>A similar function <code>grSoftVersion()</code> in package <span>grDevices</span> reports on third-party graphics software.</p>
<p>Function <code>tcltk::tclVersion()</code> reports the Tcl/Tk version.</p>
</li>
<li>Calling <code>callGeneric()</code> without arguments now works with primitive generics to some extent.</li>
<li><code>vapply(x, FUN, FUN.VALUE)</code> is more efficient notably for large <code>length(FUN.VALUE)</code>; as extension of <a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16061" target="_blank">PR#16061</a>.</li>
<li><code>as.table()</code> now allows tables with one or more dimensions of length 0 (such as <code>as.table(integer())</code>).</li>
<li><code>names(x) now clears the names of call and <code>...</code> objects.</code></li>
<li><code>library()</code> will report a warning when an insufficient dependency version is masking a sufficient one later on the library search path.</li>
<li>A new <code>plot()</code> method for class <code>"raster"</code> has been added.</li>
<li>New <code>check_packages_in_dir_changes()</code> function in package <span>tools</span> for conveniently analyzing how changing sources impacts the check results of their reverse dependencies.</li>
<li>Speed-up from Peter Haverty for <code>ls()</code> and <code>methods:::.requirePackage()</code> speeding up package loading. (<a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16133" target="_blank">PR#16133</a>)</li>
<li>New <code>get0()</code> function, combining <code>exists()</code> and <code>get()</code> in one call, for efficiency.</li>
<li><code>match.call()</code> gains an <code>envir</code> argument for specifying the environment from which to retrieve the <code>...</code> in the call, if any; this environment was wrong (or at least undesirable) when the<code>definition</code> argument was a function.</li>
<li><code>topenv()</code> has been made <code>.Internal()</code> for speedup, based on Peter Haverty&rsquo;s proposal in <a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16140" target="_blank">PR#16140</a>.</li>
<li><code>getOption()</code> no longer calls <code>options()</code> in the main case.</li>
<li>Optional use of <code>libcurl</code> (version 7.28.0 from Oct 2012 or later) for Internet access:
<ul>
<li><code>capabilities("libcurl")</code> reports if this is available.</li>
<li><code>libcurlVersion()</code> reports the version in use, and other details of the <code>"libcurl"</code> build including which URL schemes it supports.</li>
<li><code>curlGetHeaders()</code> retrieves the headers for <code>http://</code>, <code>https://</code>, <code>ftp://</code> and <code>ftps://</code> URLs: analysis of these headers can provide insights into the &lsquo;existence&rsquo; of a URL (it might for example be permanently redirected) and is so used in <code>R CMD check --as-cran</code>.</li>
<li><code>download.file()</code> has a new optional method <code>"libcurl"</code> which will handle more URL schemes, follow redirections, and allows simultaneous downloads of multiple URLs.</li>
<li><code>url()</code> has a new method <code>"libcurl"</code> which handles more URL schemes and follows redirections. The default method is controlled by a new option <code>url.method</code>, which applies also to the opening of URLs <em>via</em> <code>file()</code> (which happens implicitly in functions such as <code>read.table</code>.)</li>
<li>When <code>file()</code> or <code>url()</code> is invoked with a <code>https://</code> or <code>ftps://</code> URL which the current method cannot handle, it switches to a suitable method if one is available.</li>
</ul>
</li>
<li>(Windows.) The DLLs &lsquo;<span>internet.dll</span>&rsquo; and &lsquo;<span>internet2.dll</span>&rsquo; have been merged. In this version it is safe to switch (repeatedly) between the internal and Windows internet functions within an <strong>R</strong>session.
<p>The Windows internet functions are still selected by flag <span>&ndash;internet2</span> or <code>setInternet2()</code>. This can be overridden for an <code>url()</code> connection <em>via</em> its new <code>method</code> argument.</p>
<p><code>download.file()</code> has new method <code>"wininet"</code>, selected as the default by <span>&ndash;internet2</span> or <code>setInternet2()</code>.</p>
</li>
<li><code>parent.env&lt;-</code> can no longer modify the parent of a locked namespace or namespace imports environment. Contributed by Karl Millar.</li>
<li>New function <code>isLoadedNamespace()</code> for readability and speed.</li>
<li><code>names(env)</code> now returns all the object names of an <code>environment</code> <code>env</code>, equivalently to <code>ls(env, all.names = TRUE, sorted = FALSE)</code> and also to the names of the corresponding list,<code>names(as.list(env, all.names = TRUE))</code>. Note that although <code>names()</code> returns a character vector, the names have no particular ordering.</li>
<li>The memory manager now grows the heap more aggressively. This reduces the number of garbage collections, in particular while data or code are loaded, at the expense of slightly increasing the memory footprint.</li>
<li>New function <code>trimws()</code> for removing leading/trailing whitespace.</li>
<li><code>cbind()</code> and <code>rbind()</code> now consider S4 inheritance during S3 dispatch and also obey <code>deparse.level</code>.</li>
<li><code>cbind()</code> and <code>rbind()</code> will delegate recursively to <code>methods::cbind2</code> (<code>methods::rbind2</code>) when at least one argument is an S4 object and S3 dispatch fails (due to ambiguity).</li>
<li>(Windows.) <code>download.file(quiet = FALSE)</code> now uses text rather than Windows progress bars in non-interactive use.</li>
<li>New function <code>hsearch_db()</code> in package <span>utils</span> for building and retrieving the help search database used by <code>help.search()</code>, along with functions for inspecting the concepts and keywords in the help search database.</li>
<li>New function <code>.getNamespaceInfo()</code>, a no-check version of <code>getNamespaceInfo()</code> mostly for internal speedups.</li>
<li>The help search system now takes <span>keyword</span> entries in Rd files which are not standard keywords (as given in &lsquo;<span>KEYWORDS</span>&rsquo; in the <strong>R</strong> documentation directory) as concepts. For standard keyword entries the corresponding descriptions are additionally taken as concepts.</li>
<li>New <code>lengths()</code> function for getting the lengths of all elements in a list.</li>
<li>New function <code>toTitleCase()</code> in package <span>tools</span>, tailored to package titles.</li>
<li>The matrix methods of <code>cbind()</code> and <code>rbind()</code> allow matrices as inputs which have <em>2^31</em> or more elements. (For <code>cbind()</code>, wish of <a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16198" target="_blank">PR#16198</a>.)</li>
<li>The default method of <code>image()</code> has an explicit check for a numeric or logical matrix (which was always required).</li>
<li><code>URLencode()</code> will not by default encode further URLs which appear to be already encoded.</li>
<li><code>BIC(mod)</code> and <code>BIC(mod, mod2)</code> now give non-NA numbers for <code>arima()</code> fitted models, as <code>nobs(mod)</code> now gives the number of &ldquo;used&rdquo; observations for such models. This fixes <a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16198" target="_blank">PR#16198</a>, quite differently than proposed there.</li>
<li>The <code>print()</code> methods for <code>"htest"</code>, <code>"pairwise.htest"</code> and <code>"power.htest"</code> objects now have a <code>digits</code> argument defaulting to (a function of) <code>getOption("digits")</code>, and influencing all printed numbers coherently. Unavoidably, this changes the display of such test results in some cases.</li>
<li>Code completion for namespaces now recognizes all loaded namespaces, rather than only the ones that are also attached.</li>
<li>The code completion mechanism can now be replaced by a user-specified completer function, for (temporary) situations where the usual code completion is inappropriate.</li>
<li><code>unzip()</code> will now warn if it is able to detect truncation when unpacking a file of 4GB or more (related to <a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16243" target="_blank">PR#16243</a>).</li>
<li><code>methods()</code> reports S4 in addition to S3 methods; output is simplified when the <code>class</code> argument is used. <code>.S3methods()</code> and <code>methods::.S4methods()</code> report S3 and S4 methods separately.</li>
<li>Higher order functions such as the <code>apply</code> functions and <code>Reduce()</code> now force arguments to the functions they apply in order to eliminate undesirable interactions between lazy evaluation and variable capture in closures. This resolves <a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16093" target="_blank">PR#16093</a>.</li>
</ul><p>More at http://cran.rstudio.com/</p><p>Reference: http://www.r-bloggers.com/r-3-2-0-is-released-using-the-installr-package-to-upgrade-in-windows-os/</p>]]></description>
	<dc:creator>Neel</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37837/clipcrop-a-tool-for-detecting-structural-variations-with-single-base-resolution-using-soft-clipping-information</guid>
	<pubDate>Thu, 04 Oct 2018 16:39:28 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37837/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>This is a tool for detecting structural variations using soft-clipping information From&nbsp;<a href="http://samtools.sourceforge.net/SAM1.pdf">SAM</a>&nbsp;files.</p>
<p>https://github.com/shinout/clipcrop</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>Rahul Nayak</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22239/jrf-bioinformatics-at-national-institute-of-high-security-animal-diseases-icar</guid>
  <pubDate>Tue, 28 Apr 2015 02:21:15 -0500</pubDate>
  <link></link>
  <title><![CDATA[JRF Bioinformatics at National Institute of High Security Animal Diseases (ICAR)]]></title>
  <description><![CDATA[
<p>F.No. 4-59/2013-NIHSAD Dated: 21st April, 2015</p>

<p>SRF/ JRF job vacancies in National Institute of High Security Animal Diseases (ICAR)</p>

<p>Name of Post : JRF</p>

<p>No. of Post : 01</p>

<p>Qualification : M.V.Sc or M.Tech./M.Sc. (preferably with NET qualification) in one of following disciplines. (Biotechnology/Molecular Biology/Genetics/Microbiology/Bioinformatics or equivalent Life Sciences discipline). Desirable: Working Knowledge in the areas of Recombinant DNA Techniques, Cell Culture, Handling Laboratory Animals, Genomics.</p>

<p>Emolument : Rs.16,000/-</p>

<p>Age Limit : Up to 30 years</p>

<p>Name of Post : Project Assistant</p>

<p>No of Post : 01</p>

<p>Qualifications : First class M.Sc. /B.E/B.Tech. in one of the following disciplines Biotechnology/ Bioinformatics/ Microbiology or equivalent Life Sciences discipline). Desirable : Exposure of working in research environment, Good command over written/spoken English and computer applications.</p>

<p>Emolument : Rs.8000/-</p>

<p>Age Limit : Upto 28 years</p>

<p>Name of Post : Project Assistant</p>

<p>No of Post : 01</p>

<p>Qualification : First class M.Sc. /B.V.Sc. and A.H., B.Tech. /B.E. in Life Sciences and related areas. Desirable: Exposure of working in research environment, Good command over written/type written/spoken English and computer applications. </p>

<p>Emoluments : Rs. 8000/-</p>

<p>Age Limit : Up to 28 years<br />How to apply</p>

<p>Desirous candidates may send their applications by e-mail (techcell@hsadl.nic.in ) followed by post in the prescribed proforma latest by 11/05/2015. Walk-in-Interview will be held at NIHSAD, Kokta Road, Anand Nagar, Bhopal-462022.</p>

<p>http://www.nihsad.nic.in/pdf/Advt.pdf</p>
]]></description>
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