William asks: How can I make a graph that looks like this, “tweet density” style, showing time intervals? He then helpfully describes his input data: a CSV file with headers “time started, time finished, date”. Here’s a simple CSV file, tasks.csv: task,date,start,end task1,2010-03-05,09:00:00,13:00:00 ... [Read more...]

I’ve been vaguely aware of BioMart for a few years. Inexplicably, I’ve only recently started to use it. It’s one of the most useful applications I’ve ever used. The concept is simple. You have a set of identifiers that describe a biological object, such as a ... [Read more...]

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Yesterday, Deepak wrote about BridgeDB, a software package to deal with the “identifier mapping problem”. Put simply, biologists can name a biological entity in any way that they like, leading to multiple names for the same object. Easily solved, you might think, by choosing one identifier and sticking to it, ... [Read more...]

Andrew asks: I want to get an NCBI GEO report showing the number of samples per series or data set. Short of downloading all of GEO, anyone know how to do this? Is there a table of just metadata hidden somewhere? At work, we joke that GEO is the only ... [Read more...]

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I’m looking at ways to provide access to R via a web application. First rule: see what’s available first, before you reinvent the wheel. It’s not pretty. From the R Web Interfaces FAQ: Software Brief notes Rweb Page last updated 1999. Of the 3 example links on the page ... [Read more...]

Named rjson, appropriately. It’s quite basic just now, but contains methods for interconversion between R objects and JSON. Something like this: __ library(rjson) __ data json json [1] "{\"a\":1,\"b\":2,\"c\":3}" __ cat(json, file="data.json") Use cases? I wonder if RApache could be used to build an API that serves ... [Read more...]

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It’s been ages since I visited the R website, so I don’t know how long they’ve had a wiki. It’s built using DokuWiki, one of my personal favourites. This is a great leap forward for R documentation, which is somewhat notorious for being (a) difficult to ... [Read more...]