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Friday, September 13, 2019

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. It is so powerful and also omnipresent in high-performance computing settings (clouding computing etc). You can not survive without knowing it.

Computational biology

R programming

  • R for data science by Garrett Grolemund and Hadley Wickham.
  • Advanced R by Hadley Wickham.
  • R packages by Hadley Wickham. If you want to transit from an R user to developer, writing an R package will get you started.

Stats (R focused)

Python programming

Machine learning

Visualization

Those two books are not teaching you how to make figures programmatically (although the book by Claus was generated by Rmarkdown and the codes for all the figures can be found at https://github.com/clauswilke/dataviz). They teach you what kind of figures are informative and pleasant to eyes. From data to viz is a website guiding you to choose the right graph for your data.
I am still using R/ggplot2 for visualization.
What’s your favorite book that I have missed? Comment below!

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