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Just discovered this excellent online textbook/gitbook "Computational Genomics with R":
compgenomr.github.io/book/
principle author/editor Altuna Akalin

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@RichardJActon This is a pretty thorough book, I'm always happy to see stuff like this. It does a pretty good job at covering a bunch of epigenetics topics, too (RNA-seq, ChIP-seq, DNAme seq, etc)

@jrhawley Yes I was quite impressed by the breadth+depth combination and provides a good on-ramp for people form multiple backgrounds.
Bit light on genetic variation / mutation calling stuff at the moment but looks like chapters on specific analysis methods have been contributed by experts so more may be added. As far as I'm concerned this is how textbooks should be done now so much easier to keep them current but still citable just include the commit hash for the build your reading.

@RichardJActon Agreed. It obviously has its epigenetics focus and doesn't go into protein quantification, mutation calling, etc. But I really like the mdbook/bookdown style for in depth topics like this. It's very easy to read, it's got great support for code and figures, and supports LaTeX and footnotes! Thanks for sharing this

@RichardJActon Also, I just found that you did something similar with your thesis on your website. Nicely done, it looks great! I was thinking about doing something similar for mine when I finish my defense

@jrhawley I was just about to mention that - I basically do everything in Rmarkdown now it's awesome. Combine it with {targets} books.ropensci.org/targets/ so you can cache results of computationally intensive stuff and it's a great workflow. highly reproducible especially if you ad {renv} rstudio.github.io/renv/article and some containerization into the mix.

@jrhawley Also if you don't care so much about the static output options pdf, epub etc then you can include various widgets for interactive plots etc. Anything you can put in an {htmlwidget} htmlwidgets.org/ you can server in bookdown as a static site.

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