- EMBL Heidelberg, 15 - 16 Jan 2015
- Course Details
A laptop with a recent R (>= 3.1.1), including developer tools (for Windows, this means Rtools). See here for installation details.
To test your R installation, try the following
## If you don't have devtools
install.packages("devtools")
library("devtools")
install_github("lgatto/sequences")If you do not have any favourite editor, have a go with Rstudio.
| When | What | |
|---|---|---|
| Setup and welcome | LG | |
| 09:15 - 10:30 | OO Introduction | RS |
| Break | ||
| 11:00 - 12:30 | S3/S4 object-oriented programming | RS |
| Lunch | ||
| 13:30 - 15:30 | Package development | RS |
| Break | ||
| 16:00 - 17:30 | Advanced issues in package development and documentation | RS |
To see a full implementation of the OO and package development
material, see the sequences
package (also on CRAN).
Additional packages
install.packages(c("RUnit", "microbenchmark"))
library("BiocInstaller")
## if BiocInstaller is not installed
source("http://www.bioconductor.org/biocLite.R")
biocLite("BiocParallel")
install.packages("shiny")
## rauthoring dependencies
biocLite(c("knitr", "rmarkdown", "markdown", "ReportingTools", "DESeq2"))
library("devtools")
install_github("lgatto/rauthoring")| When | What | |
|---|---|---|
| 09:15 - 10:40 | Testing, Unit testing and debugging | LG |
| Break | ||
| 11:00 - 12:30 | Benchmarking, profiling and optimisation and calling C/C++ code | LG |
| Lunch | ||
| 13:30 - 15:30 | Vectorisation, functional programming and parallelisation (src) | LG |
| Break | ||
| 15:50 - 17:30 | R authoring and building web interfaces: shiny (vignettes in the rauthoring package) |
LG |
| Wrap up | all |
- Various teaching material: https://github.com/lgatto/teachingmaterial
- Advanced R by Hadley Wickham
- Package development
- Bioconductor package development