#The story behind the picture
Most of the common-sense ideas about therapy-related leukemia turn out to be iffy:
http://www.nature.com/nature/journal/v518/n7540/full/nature13968.html
#Bioinformatics:#
Pevzner's sequence analysis course: https://www.coursera.org/course/bioinformatics2
QB3 python for bioinformatics course: http://intro-prog-bioinfo-2014.wikispaces.com/
Harvard open courses and case studies: http://genomicsclass.github.io/book/pages/classes.html
#Writing software/libraries/packages:#
Jeff Leek's writeup: better than anything I'm likely to write.
https://github.com/jtleek/rpackages (Yes, it uses R, and since I'm trained as a statistician, so do I.)
The Python equivalent to a vignette is (roughly) the iPython notebook.
http://ipython.org/notebook.html (if you write a Python package, you should write an .ipynb using it.)
We've been containerizing analyses in Docker lately (so that BaseSpace can run them). Melissa Gymrek wrote a general overview of why this is useful: http://melissagymrek.com/science/2014/08/29/docker-reproducible-research.html
#Statistics, design of experiments, and so forth:#
Note: Substitute "data science" or whatever phrase you favor, if it makes you feel better
Tibshirani, Hastie, James & Witten's stat learning course: https://class.stanford.edu/courses/HumanitiesandScience/StatLearning/Winter2015/about
Susan Holmes' course on HMMs, R, etc.: http://web.stanford.edu/class/stats366/index.html
A list of (citable) Nature Methods feature columns: http://blogs.nature.com/methagora/2013/08/giving_statistics_the_attention_it_deserves.html
The latter is nice because you can look up specific topics by name and then cite them in rebuttals.
#Infrastructure:#
The following is mostly "how to move fast and break stuff". You may or may not want to do that. Choose wisely.
Srinivasan's startup engineering course: https://www.coursera.org/course/startup
Illumina BaseSpace developer's guide: https://developer.basespace.illumina.com/docs/content/documentation/getting-started/overview
Specifically, the Native App tutorial: https://developer.basespace.illumina.com/docs/content/documentation/native-apps/testing-and-debugging-native-app
One of these days I might properly put up my notes from last summer's bioinformatics course... (--t)
#A few useful notebooks:#
http://nbviewer.ipython.org/url/www.anamnetic.com/INTD685/AntonsAssignment.ipynb (really simple python DE)
http://nbviewer.ipython.org/url/www.anamnetic.com/INTD685/alignmentAssignment.ipynb (really needs to be updated)
http://nbviewer.ipython.org/url/goo.gl/nqhwJb (HGVS nomenclature automatically via Python package)
http://nbviewer.ipython.org/github/brentp/crystal/blob/master/notebooks/Introduction.ipynb (BrentP's crystal)