technical

A few neat tricks to make Rmarkdown reports more readable

We have recently published a Shiny (R) app called Cluster Identity Predictor (CIPR) in BMC Bioinformatics that helps annotate unknown clusters in single cell RNAseq (scRNAseq) datasets. CIPR does its thing by comparing the gene expression signatures of unknown clusters against signatures from known cell types.

Even though I do this fairly often, I keep forgeting its recipe. I might as well write it down and save time for my future self and others like me.

To understand how these algorithms work, let’s make up a toy data frame about shark attacks. Imagine that we are trying to find out the factors that are associated with the number of shark attacks at a given location.