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More hclust madness
Here is a bit of code for making a heatmap, which orders the rows of a matrix such that the first column (as ordered by in the dendrogram) has all 0s then all 1s, then the 2nd column is similarly...
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R gotchas
I put together a short list of potential R gotchas: unexpected results which might trip up new R users. For example, if we have a matrix m, m[1:2,] returns a matrix, while m[1,] returns a vector,...
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How to check your simple definition of p-value
I just read Andrew Gelman’s post about an article with his name on it starting with an inaccurate definition of p-value. I sympathize with all parties. Journalists and editors are just trying to reduce...
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How to use latex math in Rmd to display properly on GitHub Pages
Working on our PH525x online course material, Rafa and I wanted to base all lecture material in Rmd files, as these are easy for students to load into RStudio to walk through the code. Additionally,...
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RNA-seq fragment sequence bias
Our paper was just published describing a new method for modeling and correcting fragment sequence bias for estimation of transcript abundances from RNA-seq: “Modeling of RNA-seq fragment sequence bias...
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DESeq2 or edgeR
I was asked recently on Twitter about my thoughts on DESeq2 and edgeR and which tool is better. My reply was: @lpachter @gordatita_ @BioMickWatson @wolfgangkhuber perform similarly. I recommend people...
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Salmon vs kallisto on benchmarking datasets
As part of a presentation on bias modeling for RNA-seq, I put together a Shiny app that allows one to explore the differences between Salmon and kallisto on all samples from GEUVADIS and SEQC. For all...
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