Blog Archives

Balancing a centrifuge

June 11, 2016
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Balancing a centrifuge

I saw this cute little paper on arxiv about balancing a centrifuge: Peil & Hauryliuk (2010) A new spin on spinning your samples: balancing rotors in a non-trivial manner. Let us have a look at the maths of balancing a centrifuge. The way I think most people (including myself) balance their samples is to put

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Toying with models: The Game of Life with selection

February 29, 2016
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Toying with models: The Game of Life with selection

Conway’s Game of life is probably the most famous cellular automaton, consisting of a grid of cells developing according simple rules. Today, we’re going to add mutation and selection to the game, and see let patterns evolve. The fate of a cell depends on the number cells that live in the of neighbouring positions. A

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Toying with models: The Luria–Delbrück fluctuation test

February 19, 2016
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Toying with models: The Luria–Delbrück fluctuation test

I hope that Genetics will continue running expository papers about their old classics, like this one by Philip Meneely about Luria & Delbrück (1943). Luria & Delbrück performed an experiment on bacteriophage resistance in Escherichia coli, growing bacterial cultures, exposing … Läs mer →

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R in genomics @ SciLifeLab, Solna

March 24, 2015
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R in genomics @ SciLifeLab, Solna

Dear diary, I went to the Stockholm R useR group meetup on R in genomics at the Stockholm node of SciLifeLab. It was nice. If I had worked a bit closer I would attend meetups all the time. I even got to be pretentious with my notebook while waiting for the train. The speakers were:

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Finding the distance from ChIP signals to genes

July 4, 2014
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Finding the distance from ChIP signals to genes

I’ve had a couple of months off from blogging. Time for some computer-assisted biology! Robert Griffin asks on Stack Exchange about finding the distance between HP1 binding sites and genes in Drosophila melanogaster.  We can get a rough idea with some public chromatin immunoprecipitation data, R and the wonderful BEDTools. Finding some binding sites There

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More fun with %.% and %>%

March 27, 2014
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More fun with %.% and %>%

The %.% operator in dplyr allows one to put functions together without lots of nested parentheses. The flanking percent signs are R’s way of denoting infix operators; you might have used %in% which corresponds to the match function or %*% which is matrix multiplication. The %.% operator is also called chain, and what it does

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Using R: quickly calculating summary statistics (with dplyr)

March 26, 2014
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Using R: quickly calculating summary statistics (with dplyr)

I know I’m on about Hadley Wickham‘s packages a lot. I’m not the president of his fanclub, but if there is one I’d certainly like to be a member. dplyr is going to be a new and improved ddply: a package that applies functions to, and does other things to, data frames. It is also

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Using R: quickly calculating summary statistics from a data frame

March 25, 2014
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Using R: quickly calculating summary statistics from a data frame

A colleague asked: I have a lot of data in a table and I’d like to pull out some summary statistics for different subgroups. Can R do this for me quickly? Yes, there are several pretty convenient ways. I wrote about this in the recent post on the barplot, but as this is an important

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Using R: barplot with ggplot2

March 19, 2014
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Using R: barplot with ggplot2

Ah, the barplot. Loved by some, hated by some, the first graph you’re likely to make in your favourite office spreadsheet software, but a rather tricky one to pull off in R. Or, that depends. If you just need a barplot that displays the value of each data point as a bar — which is

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Morning coffee: scripting language

March 13, 2014
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Morning coffee: scripting language

Several people have asked: what scripting language should biologists learn if they are interested in doing a little larger-scale data analysis and have never programmed before? I’m not an expert, but these are the kinds of things I tend to say: The language is not so important; the same principles apply everywhere. Use what your

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