374 search results for "sweave"

Custom CSS for HTML generated using RStudio

August 26, 2012
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Custom CSS for HTML generated using RStudio

People have been telling me for a while that the latest version of RStudio, the IDE for R, is a great way to generate reports. I finally got around to trying it out and for once, the hype is justified. Start with this excellent tutorial from Jeremy Anglim. Briefly: the process is not so different

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Open Research Data Processes: KMi Crunch – Hosted RStudio Analytics Environment

August 23, 2012
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Open Research Data Processes: KMi Crunch – Hosted RStudio Analytics Environment

One of the possible barriers to widespread adoption of open notebook science is knowing where to start. Video reports of lab experiments hosted on Youtube can be easily embedded in a hosted WordPress blog; a MediaWiki wiki can be used to provide one page per experiment, with change tracking/history on each page and a shadow

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Creating beautiful reports from R with knitr

August 21, 2012
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Creating beautiful reports from R with knitr

People use the R language every day to create the elements of reports: tables, charts, analyses, and forecasts. But assembling all of that information into a print-ready document laid out with text can a hassle. You can cut-and-paste all of the elements into Word, but then what do you do when the data file gets updated at the last...

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Heatmap tables with ggplot2

August 20, 2012
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Heatmap tables with ggplot2

I wrote before about heatmap tables as a better way of producing frequency or other tables, with a solution which works nicely in latex. It is possible to do them much more easily in ggplot2, like this library(Hmisc) library(ggplot2) library(reshape) data(HairEyeColor) P=t(HairEyeColor) Pm=melt(P) ggfluctuation(Pm,type="heatmap")+geom_text(aes(label=Pm$value),colour="white")+ opts(axis.text.x=theme_text(size = 15),axis.text.y=theme_text(size = 15)) Note that ggfluctuation will also take … Continue reading...

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The Setup (Part 1)

August 16, 2012
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The Setup (Part 1)

One of the more challenging things about beginning graduate school was learning what tools and software I needed in order to work efficiently. Unlike college where software requirements were laid out in front of me and everyone seemed to use … Continue reading →

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Twitter coverage of the ISMB 2012 meeting: some statistics

August 15, 2012
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Twitter coverage of the ISMB 2012 meeting: some statistics

OK, let’s do this: some statistics and visualization of the tweets for ISMB 2012. First, thanks to Stephen Turner who got things started in this post at his excellent blog, Getting Genetics Done. Subscribe to his feed if you don’t already do so. I’ve created a Github repository for this project (and future Twitter-related work).

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Bio7 1.6 for Windows and Linux released!

August 1, 2012
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Bio7 1.6 for Windows and Linux released!

01.08.2012 Finally i released a new version of Bio7 with many improvements and new features. Updated tutorials are available, too. The new Bio7 1.6 release can be downloaded here. Please also download the examples *.zip file from the sourceforge website which contains new examples for Bio7 1.6 (e.g. an example to cluster an image folder with

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Rook rocks! Example with googleVis

August 1, 2012
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Rook rocks! Example with googleVis

What is Rook?Rook is a web server interface for R, written by Jeffrey Horner, the author of rApache and brew. But unlike other web frameworks for R, such as brew, R.rsp (which I have used in the past1), Rserve, gWidgetWWWW or sumo (which I haven't used...

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Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays

July 13, 2012
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Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays

A few years ago I was involved in analysing some time-course microarray data. Our biological collaborators were interested in how we analysed their data, so this lead to a creation of tutorial, which in turn lead to a paper. When we submitted the paper, one the referees “suggested” that we write the paper using Sweave;

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