Transcriptome feed using R

I’ve always wanted to create a transcriptome feed on Twitter, posting the results of daily PubMed searches. Well today I finally got around to it. Firstly, I made a new Twitter account; annoyingly all the Twitter handles I wanted were taken by inactive users. I decided to go with @transcriptomes. Next, I made a new…

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Calculating the h-index

Updated 2014 September 19th to include a method that does not require sorting. The h-index is an index that is calculated by measuring the number of articles, say $$n$$, that has at least $$n$$ citations. If you published 10 articles, and each of them had four citations, your h-index would be four, since there are…

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A small list of command line tips

Updated: 2014 May 14th; added even more tips I’m in the middle of writing papers and my thesis, so I’ve been quite busy. However, I wanted to write a quick blog post as an outlet. So here’s a list of random command line tips off the top of my head (GNU bash, version 4.1.2(1)-release); I…

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Sorting a huge BED file

I asked a question on Twitter about sorting a really huge file (more specifically sorting a huge BED file). To put really huge into context, the file I’m processing has 3,947,386,561 lines of genomic coordinates. I want the file to be sorted by the chromosome (lexical order), then by the start coordinate (numeric order) and…

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Student journal club

Updated 2014 March 6th: I have begun to provide summaries of papers I’ve read at my second Wiki. I have recently volunteered to organise the student journal club at my institute. I asked for the job because I am not particularly well organised, so I thought I could improve on this aspect. Another reason was…

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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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My 100th post!

Just over two years ago I started this blog and now I’m up to my 100th post! I didn’t have any particular aims or goals, I just wanted to document and share some of the things I was learning during my PhD and this still holds. Thanks to a flawed Google PageRank algorithm, my blog…

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Phylogenetic profiling

On my wiki I have a short summary of phylogenetic profiling. The program MrBayes is used for Bayesian inference for phylogeny and can be used for inferring relationships using binary type data such as phylogenetic profiles. The input to MrBayes is a NEXUS file and here is the example I will use: #NEXUS begin data;…

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