Monthly Archives: February 2015

DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis

February 28, 2015
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DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis

My R/Bioconductor package, DOSE, published in Bioinformatics. Summary: Disease ontology (DO) annotates human genes in the context of disease. DO is important annotation in translating molecular findings from high-throughput data to clinical relevance. DOSE is an R package providing semantic similarity computations among DO terms and genes which allows biologists to explore the similarities of diseases and of gene functions...

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Book Review: Mastering Scientific Computing with R

February 28, 2015
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Book Review:  Mastering Scientific Computing with R

PACKT marketing guys again contact me to review their new book Mastering Scientific Computing with R.  The book 432 pages (including covers) book is consist of 10 chapters which starts from basic R and ends with advanced data management. However, ...

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One weird trick to compile multipartite dynamic documents with Rmarkdown

February 28, 2015
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One weird trick to compile multipartite dynamic documents with Rmarkdown

This afternoon I stumbled across this one weird trick an undocumented part of the YAML headers that get processed when you click the ‘knit’ button in RStudio. Knitting turns an Rmarkdown document into a specified format, using the rmarkdown package’s render function to call pandoc (a universal document converter written in Haskell). If you...

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Playing around with #rstats twitter data

Playing around with #rstats twitter data

As a bit of weekend fun, I decided to briefly look into the #rstats twitter data that Stephen Turner collected and made available (thanks!). Essentially, this data set contains some basic information about over 100,000 tweets that contain the hashtag… Continue reading →

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Tools in Tandem – SQL and ggplot. But is it Really R?

February 28, 2015
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Tools in Tandem – SQL and ggplot. But is it Really R?

Increasingly I find that I have fallen into using not-really-R whilst playing around with Formula One stats data. Instead, I seem to be using a hybrid of SQL to get data out of a small SQLite3 datbase and into an R dataframe, and then ggplot2 to render visualise it. So for example, I’ve recently been

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Scalable Machine Learning for Big Data Using R and H2O

February 28, 2015
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Part I Part II H2O is an open source parallel processing engine for machine learning on Big Data. This prediction engine is designed by, h20, a Mountain View-based startup that has implemented a number of impressive statistical and machine learning algorithms to run on HDFS, S3, SQL and NoSQL. We were honored to have Tom Kraljevic (Vice President of...

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RcppEigen 0.3.2.4.0

February 28, 2015
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A new release of RcppEigen is now on CRAN and in Debian. It synchronizes the Eigen code with the 3.2.4 upstream release, and updates the RcppEigen.package.skeleton() package creation helper to use the kitten() function from pkgKitten for enhanced pac...

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John Snow, and Google Maps

February 27, 2015
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John Snow, and Google Maps

In my previous post, I discussed how to use OpenStreetMaps (and standard plotting functions of R) to visualize John Snow’s dataset. But it is also possible to use Google Maps (and ggplot2 types of graphs). library(ggmap) get_london <- get_map(c(-.137,51.513), zoom=17) london <- ggmap(get_london) Again, the tricky part comes from the fact that the coordinate representation system, here, is not...

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John Snow, and OpenStreetMap

February 27, 2015
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John Snow, and OpenStreetMap

While I was working for a training on data visualization, I wanted to get a nice visual for John Snow’s cholera dataset. This dataset can actually be found in a great package of famous historical datasets. library(HistData) data(Snow.deaths) data(Snow.streets) One can easily visualize the deaths, on a simplified map, with the streets (here simple grey segments, see Vincent Arel-Bundock’s...

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Data Science/Statistics/R @Google

February 27, 2015
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This meetup will be hosted by Google and we’ll have Peter Lipman and Pete Meyer...

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