Monthly Archives: May 2012

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

May 6, 2012
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Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters. The analysis module and visualization module were combined into a reusable workflow. Currently,...

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ninety two-minute r tutorial videos

May 6, 2012
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ninety two-minute r tutorial videos now posted.  three hours of ultra-concentrated r.new videos include topics like:setting your preferences (options) (Rprofile.site) random number generation (runif) (rnorm) (set.seed) (rbinom)creating and accessi...

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Online resources for handling big data and parallel computing in R

May 6, 2012
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Online resources for handling big data and parallel computing in R

by Yanchang Zhao, RDataMining.com Compared with many other programming languages, such as C/C++ and Java, R is less efficient and consumes much more memory. Fortunately, there are some packages that enables parallel computing in R and also packages for processing … Continue reading →

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Improving script_001: “Monitor”

May 6, 2012
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Improving script_001: “Monitor”

After having a look to this video: http://www.screenr.com/UxH8 from rtwotutorials, and reading some tutorials, I decided to modified the script from the previous post: Practicing Script with “ R”: Monitor , in order to make it more r...

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I’ve Converted to R Full-Time

May 6, 2012
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It's been over four years that I've been using both R and Stata, but as of last week I've become an R convert. For several years I had conducted statistical analyses in R (since many complex models can only be programmed in R), but I used Stata before ...

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reshape (from base) Explained: Part II

May 5, 2012
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reshape (from base) Explained: Part II

Part II Explains More Complex  Wide to Long With base reshape  In part I of this base reshape tutorial we went over the basics of reshaping data with reshape.  We learned two rules that help us to be more efficient … Continue reading →

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RcppArmadillo 0.3.0.3

Two days ago, Conrad Sanderson released another bug-fix version 3.0.3 for the 3.0.0 branch of his excellent Armadillo C++ template library for linear algebra. The new RcppArmadillo release 0.3.0.3 which contains it appeared on CRAN yesterday. Beside ...

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Making an Animated Heart GIF in R

May 5, 2012
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Messing around with animations, I created this toy example to make a growing outline of a heart in R. I have put it up as a gist on GitHub and embedded it below. It uses the animation and the ggplot2 packages--both of which make it incredibly simple to...

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What’s Up with Albert Pujols?

May 5, 2012
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What’s Up with Albert Pujols?

After signing a huge deal with the Angels, Pujols has been having a really bad year. He hasn't hit a home run this year, breaking a career long streak. So I thought it would be a good idea to use some statistics to tell how good or bad we think Pujols will actually be this year.Coming into the year,...

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Visualizing tables in ggplot2

May 5, 2012
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Visualizing tables in ggplot2

Recently I wanted to recreate  assocplot  using  ggplot2. In the end I propose a simple way to visualize data arranged two-way tables using geom_tile.I used Titanic data set as an example combining age and sex dimensi...

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