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Things I started to learn: - knitr, as I got sick of LaTeX (I always ended up fiddling with the figure placement forever until it was just right). I also moved
by a_bonobo 8y ago
Things I started to learn:
- knitr, as I got sick of LaTeX (I always ended up fiddling with the figure placement forever until it was just right). I also moved all my R work into RStudio, which is a HUGE time saver and the Projects function has saved me a few times.
- snakemake, for reproducible bioinformatics workflows, integrates nicely with HPC systems, and is very beautiful (the few times I've used it)
- I went through the first fast.ai course, and used it with some success on kaggle, but I'm far from doing 'bleeding edge' stuff I think (applied is fine though! give me a nice dataset and I should be fine). I've also read the Kaggle book (Deep Learning with Python), which contains a whole bunch of these weird useful machine learning tips that no-one really can't explain mathematically
- I've also made an effort to switch my R code to immediately use as much tidyverse as possible, which isn't always OK when using bioconductor at the same time
- cercatrova 8y agoCould you provide a link to the Kaggle book? A quick search reveals quite a plethora, and I'm not sure to which exactly you refer.
- a_bonobo 8y agoSorry, I confused Keras with Kaggle - holiday brain! It's this one: https://www.manning.com/books/deep-learning-with-python https://www.manning.com/books/deep-learning-with-python
- j_b_s 8y agoCurious to know why you landed on snakemake for bioinformatics? Were you considering other workflow engines?
- a_bonobo 8y agoI settled on snakemake because my corner of bioinformatics had the most prepared 'recipes' for that one, plus it played nice with our cluster's weird local flavor of SLURM