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	<title>Bioinformatics Tutorials</title>
	<link>http://www.bioinformaticstutorials.com</link>
	<description>Bioinformatics in Plain English</description>
	<lastBuildDate>Tue, 07 May 2013 19:45:49 +0000</lastBuildDate>
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	<language>en</language>
	
	<item>
		<title>Installing Birdsuite &#8211; Not Fun.</title>
		<description><![CDATA[Birdsuite is an application released by the Broad (Harvard/MIT) for analysing Affy SNP 6.0 array data. It was published in Nature Genetics. The installation process is really shockingly bad. Its a little surprising that journal like Nature Genetics can possibly justify publishing a piece of software in this condition. You would have to question whether [...]]]></description>
		<link>http://www.bioinformaticstutorials.com/?p=143</link>
			</item>
	<item>
		<title>Split a chromosome name and location type string into its constituent parts in R</title>
		<description><![CDATA[Easy to do with a regular expression and the strsplit function in R. The &#124; operator means &#8220;or&#8221;. For example for &#8220;chr15:88120587-88121480&#8243;:
> unlist(strsplit("chr15:88120587-88121480", "chr&#124;:&#124;-"))[2:4]
[1] "15"       "88120587" "88121480"
]]></description>
		<link>http://www.bioinformaticstutorials.com/?p=139</link>
			</item>
	<item>
		<title>Principal Components Analysis Explained using R</title>
		<description><![CDATA[Here, we will explain principle component analysis (PCA) by stepping though the algorithm manually and reproducing the output of the prcomp() function in R, which is normally used to do PCA.
First make up some data and plot it; in terms of gene expression analysis, we can think of the rows of the matrix below as [...]]]></description>
		<link>http://www.bioinformaticstutorials.com/?p=124</link>
			</item>
	<item>
		<title>Writing a group of R data.frames to named Excel Worksheets</title>
		<description><![CDATA[First install &#8220;WriteXLS&#8221; library in R using:
source("http://bioconductor.org/biocLite.R")
biocLite("WriteXLS")
Now if I have 3 data.frames called &#8220;genes&#8221;, &#8220;proteins&#8221; and &#8220;elephants&#8221;, all I need to do to write them to the same Excel file, on different *named* worksheets is:
library("WriteXLS")
WriteXLS(c("genes", "proteins", "elephants"), "WriteXLS.xls")
Note, for this to work, Perl needs to be installed. You also need the &#8220;Text::CSV_XS.pm&#8221; library. On Ubuntu [...]]]></description>
		<link>http://www.bioinformaticstutorials.com/?p=122</link>
			</item>
	<item>
		<title>Evolution, exercise, diet and why so many people have crooked teeth.</title>
		<description><![CDATA[Next time you walk down a crowded street, keep track of how many people look &#8220;healthy&#8221;. Why are so many people obese, have acne, are underweight or suffer from any number of diseases? We can answer this question by introducing you to the Kitava. They a hunter gatherer tribe who live in Papua New Guinea. [...]]]></description>
		<link>http://www.bioinformaticstutorials.com/?p=103</link>
			</item>
	<item>
		<title>A selfish gene theory based exlanation of rapport seeking behavior and its implications for social heirarchy in humans.</title>
		<description><![CDATA[Coming soon&#8230;
]]></description>
		<link>http://www.bioinformaticstutorials.com/?p=98</link>
			</item>
	<item>
		<title>A selfish gene theory based explaination as to why we find baby animals &#8220;cute&#8221;.</title>
		<description><![CDATA[Forewarning: To understand this article, you&#8217;re probably going to have to have read Richard Dawkins book &#8220;The Selfish Gene&#8220;. 
Kittens/puppys/ducklings/foals are undeniably cute and lovable. But why do we all think this? Ostensibly, it seems that thinking of a duckling as &#8220;cute&#8221; makes no more sense than finding a pile of bricks cute. What is [...]]]></description>
		<link>http://www.bioinformaticstutorials.com/?p=89</link>
			</item>
	<item>
		<title>Use &#8220;org.Hs.eg.db&#8221; to map between Entrez Gene Ids and HUGO gene symbols  in R</title>
		<description><![CDATA[To translate between these identifiers in R, this code creates a table with the mapping:
library(org.Hs.eg.db)
e2s = toTable(org.Hs.egSYMBOL)
To have a look at the mapping (which is stored as a data.frame)

head(e2s)

This will output something like this
  gene_id symbol
1       1   A1BG
2       2  [...]]]></description>
		<link>http://www.bioinformaticstutorials.com/?p=84</link>
			</item>
	<item>
		<title>In R, list all files in current directory ending with &#8220;.CEL&#8221;</title>
		<description><![CDATA[Use regular expression matching, where the &#8220;$&#8221; means that this string ends with the preceding string:
dir(pattern=".CEL$")
]]></description>
		<link>http://www.bioinformaticstutorials.com/?p=81</link>
			</item>
	<item>
		<title>Use biomaRt to tranlate HUGO to Entrez gene Ids.</title>
		<description><![CDATA[We can use the R package biomaRt to conveniently convert between different types of gene ids. In this example we will convert official HUGO gene names to entrez gene ids.
First we load biomaRt in R using the current ensembl database for human:
library(biomaRt)
ensembl ]]></description>
		<link>http://www.bioinformaticstutorials.com/?p=76</link>
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