Export R data to tex code

October 12, 2010
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Export R data to tex code

We often use Gnu R to work on different things and to solve various exercises. It's always a disgusting job to export e.g. a matrix with probabilities to a LaTeX document to send it to our supervisors, but Rumpel just gave me a little hint.

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ClusterProfiles

October 12, 2010
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ClusterProfiles

It is very common to cluster genes based on their expression profiles, and also very common to integrate Gene Ontology to observe the distribution of biological processes, molecular functions and cellular components for a given gene list. But, what if the two in combination? The Gene Ontology distributions across a variety of gene clusters may give us a new...

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ClusterProfiles

October 12, 2010
By
ClusterProfiles

It is very common to cluster genes based on their expression profiles, and also very common to integrate Gene Ontology to observe the distribution of biological processes, molecular functions and cellular components for a given gene list. But, what if the two in combination? The Gene Ontology distributions across a variety of gene clusters may give us a...

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Chicago Marathon 2010

October 11, 2010
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It's the Monday of the Columbus Day weekend here, so I must have been running a Chicago Marathon yesterday. Indeed -- the 34th annual Chicago Marathon took place yesterday but everything was about its 10/10/10 date. The symmetric set of numbers was i...

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Parallel processing of independent Metropolis-Hastings algorithms

October 11, 2010
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Parallel processing of independent Metropolis-Hastings algorithms

With Pierre Jacob, my PhD student, and Murray Smith, from National Institute of Water and Atmospheric Research, Wellington, who actually started us on this project at the last and latest Valencia meeting, we have completed a paper on using parallel computing in independent Metropolis-Hastings algorithms. The paper is arXived and the abstract goes as follows:

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The R-Files: Saptarshi Guha

October 11, 2010
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The R-Files: Saptarshi Guha

"The R-Files" is an occasional series from Revolution Analytics, where we profile prominent members of the R Community. Name: Saptarshi Guha Background: Ph.D. in Statistics, Purdue University Nationality: India Years Using R: 6 Known for: Developing RHIPE package for R + Hadoop integration At just 31 years old, Saptarshi Guha has emerged as a cutting-edge contributor to the R...

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R Tutorial Series: One-Way Omnibus ANOVA

October 11, 2010
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R Tutorial Series: One-Way Omnibus ANOVA

Testing the omnibus hypothesis via one-way ANOVA is simple process in R. This tutorial will explore how R can be used to perform a one-way ANOVA to test the difference between two (or more) group means. Tutorial FilesBefore we begin, you may want to do...

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R Tutorial Series: One-Way Omnibus ANOVA

October 11, 2010
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R Tutorial Series: One-Way Omnibus ANOVA

Testing the omnibus hypothesis via one-way ANOVA is simple process in R. This tutorial will explore how R can be used to perform a one-way ANOVA to test the difference between two (or more) group means. Tutorial FilesBefore we begin, you may want to do...

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New R User Group in Toronto

October 11, 2010
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Canadian R user Leo Guelman contacted me last week to ask if there was an R User Group in Toronto. There wasn't one last week, but there's one now: Leo has taken the initiative to start a new useR group. The Greater Toronto Area (GTA) R User's Group is now active on meetup.com, and taking suggestions for their first...

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How to pick the best cricketer in any format of the game?

October 11, 2010
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How to pick the best cricketer in any format of the game?

Recently ICC awards 2010 were announced and I began wondering how the process works. I haven't seen any good documentation of the process, so I started thinking  how would I do it. Here's my version. Thoughts?Note: I is impossible to det...

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How to pick the best cricketer in any format of the game?

October 11, 2010
By
How to pick the best cricketer in any format of the game?

Recently ICC awards 2010 were announced and I began wondering how the process works. I haven't seen any good documentation of the process, so I started thinking  how would I do it. Here's my version. Thoughts?Note: I is impossible to det...

Read more »

WP-CodeBox: A better R syntax highlighter plugin for WordPress

October 11, 2010
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About 10 months ago, I was looking for a plugin to enable me to highlight R code on my self hosted WordPress blog. The solution I came up with then was to use the wp-syntax plugin (with the need for some modifications). Today I was informed of (what I believe is) a better WordPress plugin

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highlight R syntax in wordpress using wp-codebox

October 10, 2010
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Tal Galili’s blog post mentioned that WP-Syntax can highlight R codes. I downloaded the modified version of WP-Syntax in his blog site. The plugin throw an error when activated. I did not try the original version hosted in WordPress. I found that WP-CodeBox use GeShi for syntax highlighting as WP-Syntax does.I used this plugin when I posted perl codes, but...

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highlight R syntax in wordpress using wp-codebox

October 10, 2010
By

Tal Galili’s blog post mentioned that WP-Syntax can highlight R codes. I downloaded the modified version of WP-Syntax in his blog site. The plugin throw an error when activated. I did not try the original version hosted in Wordpress. I found that WP-CodeBox use GeShi for syntax highlighting as WP-Syntax does.I used this plugin when I posted perl codes,...

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Nightlights in China

October 10, 2010
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Nightlights in China

Update: Some are not aware that GISS has switched to using Nightlights in the ROW. According to their updates they have moved to nightlights for the ROW. The station inventories can be found here The station I examine below is listed  like this in the new giss inventory 20551495001 TURPAN 42.92 91.00 24 384R -9MVDEno-9x-9HOT

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Le Monde puzzle [40]

October 10, 2010
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Le Monde puzzle [40]

The puzzle in Le Monde this week is called the “square five” (sic!): Two players each have twenty-five cards with five times each of the digits 1,2,3,4,5. They alternate putting one card on top of the pile, except that they can instead take an arbitrary number of consecutive cards from the top of the pile

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Data Tools Contest Update

October 10, 2010
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At midnight this morning, Kaggle began accepting submissions for the data hacking contest that we announced on Thursday. Hopefully you’ve used the last few days to build predictions for the test data set. Once you submit your predictions, you’ll be able to see your position on the leaderboard. Good luck!

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R Recommendation Contest Launches on Kaggle

October 10, 2010
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The R Recommendation Engine contest is now live on Kaggle. Please head over there and start submitting your predictions for the test data set. Once you do, you can check the leaderboard to see how your algorithm compares with other people’s work. We know that there’s still plenty of progress that can be made, because

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Add an animated R plot to your LaTeX document

October 10, 2010
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Add an animated R plot to your LaTeX document

It is possible to animate a R plot and this plot can also be exported to a LaTeX document with all its animations intact. Adding this animated plot to a PowerPoint slide or save it as a flash movie file (that you can upload to YouTube) is also possible. In this article I will try to show how these...

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Add an animated R plot to your LaTeX document

October 10, 2010
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Add an animated R plot to your LaTeX document

My first introduction with LaTeX was not very pleasant. I got tired and frustrated by writing so many codes for producing a simple document; but a few days ago I could write a function for producing an animated plot in R and also could export it to my LaTeX document with all its animations intact (using animation package of...

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dcemriS4 0.34

October 9, 2010
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The R package dcemriS4 is a collection of functions, with examples and documentation, that allows one to perform voxel-wise quantitative analysis of dynamic contrast-enhanced MRI (DCE-MRI) or diffusion-weighted imaging (DWI) data.  The primary app...

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dcemriS4 0.34

October 9, 2010
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The R package dcemriS4 is a collection of functions, with examples and documentation, that allows one to perform voxel-wise quantitative analysis of dynamic contrast-enhanced MRI (DCE-MRI) or diffusion-weighted imaging (DWI) data.  The primary app...

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oro.nifti 0.2.1

October 9, 2010
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The R package oro.nifti contains functions for the input/output and visualization of medical imaging data that follow either the ANALYZE or NIfTI formats.  This package is part of the Rigorous Analytics bundle.The latest version of oro.nifti (0....

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oro.nifti 0.2.1

October 9, 2010
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The R package oro.nifti contains functions for the input/output and visualization of medical imaging data that follow either the ANALYZE or NIfTI formats.  This package is part of the Rigorous Analytics bundle.The latest version of oro.nifti (0....

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oro.dicom 0.2.7

October 9, 2010
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The R package oro.dicom contains functions for the input/output of medical imaging data that conform to the Digital Imaging and Communications in Medicine (DICOM) standard.  This package is part of the Rigorous Analytics bundle. The latest version...

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oro.dicom 0.2.7

October 9, 2010
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The R package oro.dicom contains functions for the input/output of medical imaging data that conform to the Digital Imaging and Communications in Medicine (DICOM) standard.  This package is part of the Rigorous Analytics bundle. The latest version...

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A competition to recommend “relevant” R packages – and the future of R

October 9, 2010
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Update: the competition was just launched. * * * What is the competition about? Drew Conway and John Myles Whyte have collected data from (52) R users about the packages they have installed. The data is now available on github for download and the contest will be run on the kaggle platform. For more details,

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Mapping BioStar users onto the world map

October 9, 2010
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Mapping BioStar users onto the world map

Neil is my new bioinformatics hero! (Sorry Pierre :)BioStar is a Q&A website for bioinformatics, just like the Blue Obelisk eXchange. Neil and Pierre have an ongoing struggle to gain the most karma, requiring Pierre to put in a formal complaint aga...

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BioStar users (of the world, unite)

October 9, 2010
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BioStar users (of the world, unite)

Egon writes: Can someone please plot the BioStar users on a Google Map? Sounds like a challenge. Let’s go. 1. Harvesting user IP addresses BioStar user profiles (here’s mine) include a location field. It’s free text and optional, which means that location is missing or inaccurate for many users. However, if you’re logged into BioStar

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