375 search results for "sweave"

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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Rchievement of the day #3: Bloggin’ from R

July 1, 2012
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Rchievement of the day #3: Bloggin’ from R

I have become a complete knitr addict of late and have been using it in combination with RStudio’s R markdown support on a regular basis. In fact I wrote this post using it! It then dawned on me how great it would be if I … Continue reading →

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reproducible documents/analytics in R: the knitr package

June 26, 2012
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reproducible documents/analytics in R: the knitr package

When I am working in new institutions and I am asking: “Do you have a document management system?” I often get the answer:”Yap, we are using folders” … OKAY. Making analysis, developing applications and keeping an eye on code, data and applications make this even harder as it has to be. Of course not many

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Making Reproducible Research Enjoyable

June 25, 2012
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Making Reproducible Research Enjoyable

Note: this is a contributed article for the ICSA Bulletin and the basic idea can be summarized in this picture. It is hard to convince people to think about reproducible research (RR). There are two parts of difficulties: (1) tools used to be for ex...

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useR 2012: main conference braindump

June 24, 2012
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useR 2012: main conference braindump

I knew R was versatile, but DANG, people do a lot with it: > > … I don’t think anyone actually believes that R is designed to make *everyone* happy. For me, R does about 99% of the things I … Continue reading →

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Highlights of the useR! 2012 – Review of the reviews

June 24, 2012
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Highlights of the useR! 2012 – Review of the reviews

It’s gutted that I could not attend useR! 2012 after having a great time at useR!2011 at Warwick. However, a great active online community of useRs allows me to get lots of goods stuffs from the conference even though I did not attend physically. By keep following the #useR2012 and #rstats in Twitter and reading some great posts from R-bloggerRs on the

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Reproducible reports & research with knitr in R Studio

June 18, 2012
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Reproducible reports & research with knitr in R Studio

Arguably, knitr (CRAN link) is the most outstanding R package of this year and its creator, Yihui Xie is the star of the useR! conference 2012. This is because the ease of use comparing to Sweave for making reproducible report. Integration of knitR and R Studio has made reproducible research much more convenience, intuitive and easier to

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Data on GitHub: The easy way to make your data available

June 13, 2012
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Data on GitHub: The easy way to make your data available

GitHub is designed for collaborating on coding projects. Nonetheless, it is also a potentially great resource for researchers to make their data publicly available. Specifically you can use it to:store data in the cloud for future use (for free),track ...

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Quickly use googleVis in web reports using Tiki and PluginR

June 12, 2012
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Quickly use googleVis in web reports using Tiki and PluginR

R is hot and amazing. Tiki is too And with PluginR, we can easily place in simple or advanced web reports any R code, in a similar fashin to what can be achieved with other longer combinations (Sweave, Knitr, ... and latex). For instance, I tried a few days ago to quickly...

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Making interactive slides with Org mode and googleVis in R

June 3, 2012
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Making interactive slides with Org mode and googleVis in R

There’s been a lot of justifiable excitement in the R community about Yihui Xie’s great work, and most recently the incorporation of his knitr package into the RStudio software. Knitr is seen, justifiably, as a worthy successor to SWeave for … Continue reading →

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