Blog Archives

ggheat : a ggplot2 style heatmap function

March 11, 2011
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ggheat  :  a ggplot2 style heatmap function

I hope the code here is fairly self-explanatory with the inset annotations. I feel this is just a bit 'prettier' than heatmap.2 and has for me the right balance of options and extensibility. I have also found it difficult to produce high quality plots...

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I love RStudio

March 1, 2011
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I love RStudio

Typically if I am working with R I will have a lot of different windows open all at once. I'll have the R Console (for Mac) of course and a text editor (Xcode or TextEdit), plus there will usually be some help windows to examine particular functions o...

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(more on) Pattern Matching for Transcription Factor Binding Sites

February 2, 2011
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I have published some initial script scribblings on this task about a week ago. After another week I'm posting some better formed and annotated code. The Biostrings and BSGenomes packages are new to me and I've gone through many many iterations and ex...

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DataMarket

January 31, 2011
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I have just discovered yet another public data site www.datamarket.com. Most of the data are time-series. It collects together things like World bank, Eurostat, Gapminder into the one place. It also allows you to download data as csv files or to creat...

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Pattern Matching for Transcription Factor Binding Sites

January 24, 2011
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I'm trying to search for binding sites for the transcription factor MAF (i.e. TFBS for MAF) in the promoter regions of various genes. I initially started out looking at a precomputed database of binding sites MAPPER. However the TFBS models that have ...

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gnmplot

January 13, 2011
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gnmplot

I'm writing a new package that will create nice publication quality graphics of genome information. It's really an adaptor sitting between the biomaRt and ggplot2 packages. Here is the code so far: ## this function integrates 3 steps to creating a g...

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prettyR

January 13, 2011
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I have just remembered a package called 'prettyR' that pretty much does what it says. It makes R code more readable.. so an example from my forthcoming genomeplot package (see forthcoming blog entry):   ## this function integrates 3 steps to creat...

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survival curves for Leonid

January 7, 2011
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survival curves for Leonid

Leonid asked me to do a quick survival analysis of two different types of mouse (m430 and m210) with surgically implanted tumours (or something like that). The data was in the wrong format but after transforming it looked like this: In my opini...

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