Venue
Skaggs building, 114.
Requirements
If you want to follow along, please bring a laptop with R (first day) and a SSH client. Software for the second day will be discussed at the end of the first day.
Day 1
| Time | Presenter | Topic |
|---|---|---|
| 8.30 | Tiago | Introduction and DBS Scientific computing architecture |
| 9.00 | Brice | Selected Unix topics: user profiles, persistent shells, parallelization, evaluating available resources, submission to the SRA, etc. |
| 11.00 | Break | |
| 11.15 | Travis | Efficient computing, and how terminal commands can simplify your life |
| 01.00 | Break | |
| 02.00 | Brice | Selected R topics: Installing to local repositories, functions, environments, parallelization, condition handling, etc. |
| 03.45 | Christian | R data.table: Big Fast Data |
| 04.30 | Break | |
| 04.45 | Tiago | Introducing the Python environment (Jupyter lab, matplotlib, Python3, conda) |
| 05.30 | End |
Day 2
| Time | Presenter | Topic |
|---|---|---|
| 08.30 | Brice | R: Wrap up and case study examples |
| 09.15 | Tiago | Data preprocessing (HDF5, VCF) |
| 11.00 | Break | |
| 11.15 | Tiago | Parallel processing with Dask, subsampling |
| 01.00 | Break | |
| 02.00 | ||
| 02.45 | Doug | Montana code |
| 03.00 | Break | |
| 03.15 | Tiago | Galaxy programmatic interface |
| 05.30 | End |
Links
- R
- The R Inferno: Fun and Informative. "If you are using R and you think you’re in hell, this is a map for you."
- Google R style guide: Write cleaner code!
- CRAN FAQs: Details, including OSX, Windows.
- Advanced R: Superior R learning material from Hadley Wickham.