Kategoriarkiv: data analysis

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 … Läs mer

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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 … Läs mer

Publicerat i computer stuff, data analysis, english, genetik | Märkt , , , , | 1 kommentar

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 %*% … Läs mer

Publicerat i computer stuff, data analysis, english | Märkt , | 7 kommentarer

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 … Läs mer

Publicerat i computer stuff, data analysis, english | Märkt , | 2 kommentarer

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 … Läs mer

Publicerat i computer stuff, data analysis, english | Märkt , , , | 8 kommentarer

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 … Läs mer

Publicerat i computer stuff, data analysis, english | Märkt , , , , | 2 kommentarer

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 … Läs mer

Publicerat i computer stuff, data analysis, english, morning coffee | Märkt , | 3 kommentarer