<?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/37586?offset=210</link>
	<atom:link href="https://bioinformaticsonline.com/related/37586?offset=210" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44633/learn-python-with-example</guid>
	<pubDate>Tue, 06 Aug 2024 23:51:51 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44633/learn-python-with-example</link>
	<title><![CDATA[Learn python with example]]></title>
	<description><![CDATA[<div><div><div><p>There are over 21 unique&nbsp;Python project&nbsp;walkthroughs in this content that range from beginner to advanced. See below for the timestamps for these projects:</p><p><span>00:00:00 | How To Navigate These Projects</span><br /><span>---</span><br /><span>00:01:46 | #1 - Quiz Game (Easy)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2Fblob%2Fmain%2Fquiz_game.py" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/quiz_game.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>00:22:00 | #2 - Number Guessing Game (Easy)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2Fblob%2Fmain%2Fnumber_guesser.py" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/number_guesser.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>00:39:49 | #3 - Rock, Paper, Scissors (Easy)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2Fblob%2Fmain%2Frock_paper_scissors.py" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/rock_paper_scissors.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>00:54:40 | #4 - Choose Your Own Adventure Game (Easy)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2Fblob%2Fmain%2Fchoose_your_own_adventure.py" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/choose_your_own_adventure.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>01:06:47 | #5 - Password Manager (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2F" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/</a><span>&nbsp;</span><br /><span>Fernet Cryptography Documentation:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fcryptography.io%2Fen%2Flatest%2Ffernet%2F" target="_blank">https://cryptography.io/en/latest/fernet/</a><span>&nbsp;</span><br /><span>---</span><br /><span>01:37:37 | #6 - PIG (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects%2Fblob%2Fmain%2Fproject1.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project1.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>01:59:07 | #7 - Madlibs Generator (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects%2Fblob%2Fmain%2Fproject2.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project2.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>02:15:04 | #8 - Timed Math Challenge (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects%2Fblob%2Fmain%2Fproject3.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project3.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>02:28:02 | #9 - Slot Machine (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Slot-Machine" target="_blank">https://github.com/techwithtim/Python-Slot-Machine</a><span>&nbsp;</span><br /><span>---</span><br /><span>03:20:43 | #10 - Turtle Racing (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FTurtle-Racing-V2" target="_blank">https://github.com/techwithtim/Turtle-Racing-V2</a><span>&nbsp;</span><br /><span>Turtle Docs:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fdocs.python.org%2F3%2Flibrary%2Fturtle.html" target="_blank">https://docs.python.org/3/library/turtle.html</a><span>&nbsp;</span><br /><span>---</span><br /><span>04:13:09 | #11 - WPM Typing Test (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FWPM_Typing_Test" target="_blank">https://github.com/techwithtim/WPM_Typing_Test</a><span>&nbsp;</span><br /><span>Curses Docs:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fdocs.python.org%2F3%2Fhowto%2Fcurses.html" target="_blank">https://docs.python.org/3/howto/curses.html</a><span>&nbsp;</span><br /><span>05:09:43 | #12 - Alarm Clock (Easy)</span><br /><span>Python Project Idea Blog:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fhackr.io%2Fblog%2Fpython-projects" target="_blank">https://hackr.io/blog/python-projects</a><span>&nbsp;</span><br /><span>Sound Effects:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fwww.fesliyanstudios.com%2Froyalty-free-sound-effects-download%2Falarm-203" target="_blank">https://www.fesliyanstudios.com/royalty-free-sound-effects-download/alarm-203</a><span>&nbsp;</span><br /><span>---</span><br /><span>05:22:07 | #13 - Password Generator (Easy)</span><br /><span>Python Project Idea Blog:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fhackr.io%2Fblog%2Fpython-projects" target="_blank">https://hackr.io/blog/python-projects</a><span>&nbsp;</span><br /><span>---</span><br /><span>05:39:16 | #14 - Shortest Path Finder (Advanced)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects-For-Intermediates%2Fblob%2Fmain%2Fpath-finder.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/path-finder.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>06:14:53 | #15 - NBA Stats &amp; Current Scores (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects-For-Intermediates%2Fblob%2Fmain%2Fnba-scores.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/nba-scores.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>06:38:22 | #16 - Currency Converter (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects-For-Intermediates%2Fblob%2Fmain%2Fcurrency-converter.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/currency-converter.py</a><span>&nbsp;</span><br /><span>API: https://free.currencyconverterapi.com/</span><br /><span>---</span><br /><span>06:58:51 | #17 - YouTube Video Downloader (Medium)</span><br /><span>Code: &nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Beginner-Automation-Projects%2Fblob%2Fmain%2Fyoutube.py" target="_blank">https://github.com/techwithtim/Python-Beginner-Automation-Projects/blob/main/youtube.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>07:09:50 | #18 - Automated File Backup (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Beginner-Automation-Projects%2Fblob%2Fmain%2Fbackup.py" target="_blank">https://github.com/techwithtim/Python-Beginner-Automation-Projects/blob/main/backup.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>07:21:18 | #19 - Mastermind/4 Color Match (Advanced)</span><br /><span>---</span><br /><span>07:48:20 | #20 - Aim Trainer (Advanced)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Aim-Trainer" target="_blank">https://github.com/techwithtim/Python-Aim-Trainer</a><span>&nbsp;</span><br /><span>---</span><br /><span>08:39:20 | #21 - Advanced Python Scripting (Advanced)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Scripting-Project" target="_blank">https://github.com/techwithtim/Python-Scripting-Project</a><span>&nbsp;</span></p></div></div></div>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/36502/creating-conda-environment-for-python27</guid>
	<pubDate>Mon, 07 May 2018 08:56:52 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/36502/creating-conda-environment-for-python27</link>
	<title><![CDATA[Creating conda environment for python2.7]]></title>
	<description><![CDATA[<p>TIP: By default, environments are installed into the&nbsp;<code><span>envs</span></code>&nbsp;directory in your conda directory. Run&nbsp;<code><span>conda</span>&nbsp;<span>create</span>&nbsp;<span>--help</span></code>&nbsp;for information on specifying a different path.</p><p>Use the Terminal or an Anaconda Prompt for the following steps.</p><ol>
<li>
<p>To create an environment:</p>
<div>
<div>
<pre><span></span><span>conda</span> <span>create</span> <span>--</span><span>name</span> <span>myenv</span>
</pre>
</div>
</div>
<p>NOTE: Replace&nbsp;<code><span>myenv</span></code>&nbsp;with the environment name.</p>
</li>
<li>
<p>When conda asks you to proceed, type&nbsp;<code><span>y</span></code>:</p>
<div>
<div>
<pre><span></span>proceed ([y]/n)?
</pre>
</div>
</div>
</li>
</ol><p>This creates the myenv environment in&nbsp;<code><span>/envs/</span></code>. This environment uses the same version of Python that you are currently using, because you did not specify a version.</p><p>To create an environment with a specific version of Python:</p><div><div><pre><span></span>conda create -n myenv <span>python</span><span>=</span><span>3</span>.4
</pre></div></div><p>To create an environment with a specific package:</p><div><div><pre><span></span>conda create -n myenv scipy
</pre></div></div><p>OR:</p><div><div><pre><span></span>conda create -n myenv python
conda install -n myenv scipy
</pre></div></div><p>To create an environment with a specific version of a package:</p><div><div><pre><span></span>conda create -n myenv <span>scipy</span><span>=</span><span>0</span>.15.0
</pre></div></div><p>OR:</p><div><div><pre><span></span>conda create -n myenv python
conda install -n myenv <span>scipy</span><span>=</span><span>0</span>.15.0
</pre></div></div><p>To create an environment with a specific version of Python and multiple packages:</p><div><div><pre><span></span>conda create -n myenv <span>python</span><span>=</span><span>3</span>.4 <span>scipy</span><span>=</span><span>0</span>.15.0 astroid babel
</pre></div></div><p>TIP: Install all the programs that you want in this environment at the same time. Installing 1 program at a time can lead to dependency conflicts.</p><p>To automatically install pip or another program every time a new environment is created, add the default programs to the&nbsp;<a href="https://conda.io/docs/user-guide/configuration/use-condarc.html#config-add-default-pkgs">create_default_packages</a>&nbsp;section of your&nbsp;<code><span>.condarc</span></code>&nbsp;configuration file. The default packages are installed every time you create a new environment. If you do not want the default packages installed in a particular environment, use the&nbsp;<code><span>--no-default-packages</span></code>&nbsp;flag:</p><div><div><pre><span></span>conda create --no-default-packages -n myenv python
</pre></div></div><p>TIP: You can add much more to the&nbsp;<code><span>conda</span>&nbsp;<span>create</span></code>&nbsp;command. For details, run&nbsp;<code><span>conda</span>&nbsp;<span>create</span>&nbsp;<span>--help</span></code>.</p><p>➜ redundans git:(master) ✗ conda create --name py27 python=2.7<br />Solving environment: done</p><p><br />==&gt; WARNING: A newer version of conda exists. &lt;==<br /> current version: 4.5.0<br /> latest version: 4.5.2</p><p>Please update conda by running</p><p>$ conda update -n base conda</p><p>&nbsp;</p><p>## Package Plan ##</p><p>environment location: /home/urbe/anaconda3/envs/py27</p><p>added / updated specs: <br /> - python=2.7</p><p><br />The following packages will be downloaded:</p><p>package | build<br /> ---------------------------|-----------------<br /> wheel-0.31.0 | py27_0 61 KB<br /> python-2.7.15 | h1571d57_0 12.1 MB<br /> certifi-2018.4.16 | py27_0 142 KB<br /> sqlite-3.23.1 | he433501_0 1.5 MB<br /> setuptools-39.1.0 | py27_0 582 KB<br /> openssl-1.0.2o | h20670df_0 3.4 MB<br /> pip-10.0.1 | py27_0 1.7 MB<br /> ca-certificates-2018.03.07 | 0 124 KB<br /> ------------------------------------------------------------<br /> Total: 19.6 MB</p><p>The following NEW packages will be INSTALLED:</p><p>ca-certificates: 2018.03.07-0 <br /> certifi: 2018.4.16-py27_0 <br /> libedit: 3.1-heed3624_0 <br /> libffi: 3.2.1-hd88cf55_4 <br /> libgcc-ng: 7.2.0-hdf63c60_3 <br /> libstdcxx-ng: 7.2.0-hdf63c60_3 <br /> ncurses: 6.0-h9df7e31_2 <br /> openssl: 1.0.2o-h20670df_0<br /> pip: 10.0.1-py27_0 <br /> python: 2.7.15-h1571d57_0<br /> readline: 7.0-ha6073c6_4 <br /> setuptools: 39.1.0-py27_0 <br /> sqlite: 3.23.1-he433501_0<br /> tk: 8.6.7-hc745277_3 <br /> wheel: 0.31.0-py27_0 <br /> zlib: 1.2.11-ha838bed_2</p><p>Proceed ([y]/n)? y</p><p><br />Downloading and Extracting Packages<br />wheel 0.31.0: #################################################################################################################################################################################################### | 100% <br />python 2.7.15: ################################################################################################################################################################################################### | 100% <br />certifi 2018.4.16: ############################################################################################################################################################################################### | 100% <br />sqlite 3.23.1: ################################################################################################################################################################################################### | 100% <br />setuptools 39.1.0: ############################################################################################################################################################################################### | 100% <br />openssl 1.0.2o: ################################################################################################################################################################################################## | 100% <br />pip 10.0.1: ###################################################################################################################################################################################################### | 100% <br />ca-certificates 2018.03.07: ###################################################################################################################################################################################### | 100% <br />Preparing transaction: done<br />Verifying transaction: done<br />Executing transaction: done<br />#<br /># To activate this environment, use:<br /># &gt; source activate py27<br />#<br /># To deactivate an active environment, use:<br /># &gt; source deactivate<br />#</p><p>➜ redundans git:(master) ✗ source activate py27</p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44179/python-mini-projects</guid>
	<pubDate>Mon, 16 Jan 2023 02:14:03 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44179/python-mini-projects</link>
	<title><![CDATA[Python Mini Projects !]]></title>
	<description><![CDATA[<p><span>There is a directory for each chapter of the book. Each directory contains a&nbsp;</span><code>test.py</code><span>&nbsp;program you can use with&nbsp;</span><code>pytest</code><span>&nbsp;to check that you have written the program correctly. I have included a short README to describe each exercise. If you have problems writing code (or if you would like to support this project!), the book contains details about the skills you need.</span></p>
<p>https://github.com/kyclark/tiny_python_projects</p><p>Address of the bookmark: <a href="https://github.com/kyclark/tiny_python_projects" rel="nofollow">https://github.com/kyclark/tiny_python_projects</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/120/user</guid>
	<pubDate>Wed, 10 Jul 2013 14:41:49 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/120/user</link>
	<title><![CDATA[useR!]]></title>
	<description><![CDATA[<p><span>The R project actively supports two conference series, organized regularly by members from the R community: useR! - providing a forum to the R user community - and DSC - a platform for developers of statistical software.</span></p><p><span>Recently useR! conference have been organized&nbsp;<span>University of Castilla-La Mancha, Albacete, Spain.</span></span></p><p><a href="http://www.edii.uclm.es/~useR-2013//">http://www.edii.uclm.es/~useR-2013//</a></p><p>&nbsp;</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</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/news/view/8848/upgrade-r-303</guid>
	<pubDate>Mon, 10 Mar 2014 11:23:51 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/8848/upgrade-r-303</link>
	<title><![CDATA[Upgrade R 3.0.3]]></title>
	<description><![CDATA[<p>R is a free software programming language and software environment for statistical computing and graphics. The R language is widely used among statisticians and data miners for developing statistical software and data analysis. Polls and surveys of data miners are showing R's popularity has increased substantially in recent years. Recently the new version of R codename &ldquo;Warm Puppy" have been released.<br /><br />You can download the latest version from here http://cran.rstudio.com/ . Or, if you are using Windows, you can upgrade to the latest version using the installr package http://cran.r-project.org/web/packages/installr/ . Simply run the following code:<br /><br /># installing/loading the package:<br />if(!require(installr)) { <br />install.packages("installr"); require(installr)} #load / install+load installr<br />&nbsp;<br />updateR()<br /><br />I try to keep the installr package updated and useful. If you have any suggestions or remarks on the package, you&rsquo;re invited to leave a comment below.<br /><br />If you use the global library system http://www.r-statistics.com/2010/04/changing-your-r-upgrading-strategy-and-the-r-code-to-do-it-on-windows/ , you can run the following in the new version of R:<br /><br />source("http://www.r-statistics.com/wp-content/uploads/2010/04/upgrading-R-on-windows.r.txt")<br />New.R.RunMe()</p><p>Reference:</p><p>http://www.r-statistics.com/2014/03/r-3-0-3-is-released/</p>]]></description>
	<dc:creator>Rahul Nayak</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/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>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/26573/efficient-genome-searching-with-biostrings-and-the-bsgenome-data-package</guid>
	<pubDate>Mon, 07 Mar 2016 05:18:06 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/26573/efficient-genome-searching-with-biostrings-and-the-bsgenome-data-package</link>
	<title><![CDATA[Efficient genome searching with Biostrings and the BSgenome data package]]></title>
	<description><![CDATA[<p>Address of the bookmark: <a href="https://www.bioconductor.org/packages/3.3/bioc/vignettes/BSgenome/inst/doc/GenomeSearching.pdf" rel="nofollow">https://www.bioconductor.org/packages/3.3/bioc/vignettes/BSgenome/inst/doc/GenomeSearching.pdf</a></p>]]></description>
	<dc:creator>Aasha</dc:creator>
</item>

</channel>
</rss>