Visualization

My opinionated selection of books/urls for bioinformatics/data science curriculum

There was a paper on this topic: A New Online Computational Biology Curriculum. I am going to provide a biased list below (I have read most of the books if not all). I say it is biased because you will see many books of R are from Hadely Wickham. I now use tidyverse most of the time. Unix I suggest people who want to learn bioinformatics starting to learn unix commands first.

plot 10x scATAC coverage by cluster/group

This post was inspired by Andrew Hill’s recent blog post. Inspired by some nice posts by @timoast and @tangming2005 and work from @10xGenomics. Would still definitely have to split BAM files for other tasks, so easy to use tools for that are super useful too! — Andrew J Hill (@ahill_tweets) April 13, 2019 Andrew wrote that blog post in light of my other recent blog post and Tim’s (developer of the almighty Seurat package) blog post.

A tale of two heatmap functions

You probably do not understand heatmap! Please read You probably don’t understand heatmaps by Mick Watson In the blog post, Mick used heatmap function in the stats package, I will try to walk you through comparing heatmap, and heatmap.2 from gplots package. Before I start, I want to quote this: “The defaults of almost every heat map function in R does the hierarchical clustering first, then scales the rows then displays the image”