Blog Archives

How to build a Shiny app for disease- & trait-associated locations of the human genome

December 17, 2016
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This app is based on the gwascat R package and its ebicat38 database and shows trait-associated SNP locations of the human genome. You can visualize and compare the genomic locations of up to 8 traits simultaneously. The National Human Genome Research...

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Gene homology Part 2 – creating directed networks with igraph

December 13, 2016
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Gene homology Part 2 – creating directed networks with igraph

In my last post I created a gene homology network for human genes. In this post I want to extend the network to include edges for other species. First, I am loading biomaRt and extract a list of all available datasets. library(biomaRt) ensembl = useM...

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Creating a network of human gene homology with R and D3 (without html widget for easy loading)

December 11, 2016
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Creating a network of human gene homology with R and D3 (without html widget for easy loading)

The html widget I produced with networksD3 seems to create problems with loading the site for some people, so here is the same blog post as yesterday just without the rendered html widget in it. This week I want to explore how many of our human ge...

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How to set up your own R blog with Github pages and Jekyll Bootstrap

December 3, 2016
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How to set up your own R blog with Github pages and Jekyll Bootstrap

This post is in reply to a request: How did I set up this R blog? I have wanted to have my own R blog for a while before I actually went ahead and realised this page. I had seen all the cool things people do with R by following R-bloggers and reading ...

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Extreme Gradient Boosting and Preprocessing in Machine Learning – Addendum to predicting flu outcome with R

December 1, 2016
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Extreme Gradient Boosting and Preprocessing in Machine Learning – Addendum to predicting flu outcome with R

In last week’s post I explored whether machine learning models can be applied to predict flu deaths from the 2013 outbreak of influenza A H7N9 in China. There, I compared random forests, elastic-net regularized generalized linear models, k-nearest ne...

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Can we predict flu deaths with Machine Learning and R?

November 26, 2016
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Can we predict flu deaths with Machine Learning and R?

Among the many R packages, there is the outbreaks package. It contains datasets on epidemics, on of which is from the 2013 outbreak of influenza A H7N9 in China, as analysed by Kucharski et al. (2014): A. Kucharski, H. Mills, A. Pinsent, C. Fraser,...

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Analysing the Gilmore Girls’ coffee addiction with R

November 21, 2016
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Analysing the Gilmore Girls’ coffee addiction with R

Last week’s post showed how to create a Gilmore Girls character network. In this week’s short post, I want to explore the Gilmore Girls’ famous coffee addiction by analysing the same episode transcripts that were also used last week. I am also ...

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Creating a Gilmore Girls character network with R

November 12, 2016
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Creating a Gilmore Girls character network with R

With the impending (and by many - including me - much awaited) Gilmore Girls Revival, I wanted to take a somewhat different look at our beloved characters from Stars Hollow. I had recently read a few cool examples of how to create co-occurrence networ...

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Is ‘Yeah’ Josh and Chuck’s favorite word?

November 5, 2016
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Is ‘Yeah’ Josh and Chuck’s favorite word?

Text mining and sentiment analysis of a Stuff You Should Know Podcast Stuff You Should Know (or SYSK) is one of the many great podcasts from How Stuff Works. The two SYSK hosts Josh and Chuck have taught me so many fascinating things over the years,...

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Exploring the human genome (Part 2) – Transcripts

October 31, 2016
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Exploring the human genome (Part 2) – Transcripts

How many transcripts and proteins do genes have? In Exploring the human genome (Part 1) - Gene Annotations I examined Ensembl, Entrez and HGNC gene annotations with AnnotationDbi via three R packages: org.Hs.eg.db, EnsDb.Hsapiens.v79 and TxDb.Hsapiens...

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