Blog Archives

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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Using R: common errors in table import

March 6, 2014
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Using R: common errors in table import

I’ve written before about importing tabular text files into R, and here comes some more. This is because I believe (firmly) that importing data is the major challenge for beginners who want to analyse their data in R. What is the most important thing about using any statistics software? To get your data into it

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