Querying PubMed using R

I’ve seen talks over the years where the speaker shows a bar chart with the number of articles in PubMed that contain a certain keyword and tallied per year. In most of the cases the speaker was trying to illustrate the growing number of articles that contain the keyword. Here I try to do the…

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Using the R twitteR package

Updated 2014 November 26th to reflect changes in the tm package Updated 2015 February 18th to reflect changes in the twitteR package A short post on using the R twitteR package for text mining and using the R wordcloud package for visualisation. I did this on my Windows machine, which has this problem. I’ve updated…

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10,000 monthly visitors, apparently

I created davetang.org on the 24th of April 2009 just for the sake of buying a domain with my name in it. Realising that I was and am paying for a service, I decided to actually make use of my web space. But it really started to become handy when I decided to pursue a…

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Kobe Byrant and the 2012 Lakers

Kobe Byrant and the Lakers (11-14) aren’t doing as well as I had expected given the team they acquired in the off season. Everyone likes to point out that when he scores over x number of points (e.g. 30), the Lakers have lost more than they have won. So I took his stats for this…

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Explaining PCA to a school child

Ed Yong asked on Twitter “Explain principal component analysis to a schoolchild in a tweet.” Since I can’t explain PCA eloquently, I found this interesting and wanted to keep a record of the replies for future reference. Here are some of the modified replies, with my favourite first (and the rest in no particular order):…

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Silly mnemonics

Back in first year genetics (i.e. genetics 101), our tutor was telling us of a way to remember pyrimidines and purines. She said, pyrimidines reminded her of the pyramids and therefore Cleopatra and Tutankhamun and therefore Cytosines and Thymines. We laughed, but to this day that’s how I remember pyrimidines. Another thing I keep forgetting…

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DropBox offering up to 5GB worth of space

From the official DropBox forum: During this beta period, we are also offering additional free space to test automatic uploading of photos and videos. For every 500MB of photos and videos automatically uploaded, you’ll receive another 500MB space bonus, up to 5GB total. More information here. Here’s some R code I used to generate some…

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Using Velvet

Write script for generating random tags from a longer piece of DNA Generate random tags and use as input for velvet I don’t know why in the definition line reads length = 480 (NODE_1_length_480) when the contig length is 500. BLAST the contig back to the original sequence Score = 924 bits (500), Expect =…

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