Bioinformatics: Command Line/R Prerequisites Online
Oct. 5, 2020, 9 a.m. - Oct. 9, 2020, 5 p.m.
Organizer -
Bioinformatics Core
Contact -
UC Davis Bioinformatics Core, training.bioinformatics@ucdavis.edu
Listed topics are preliminary and subject to change. For documentation from previous workshops, visit http://bioinformatics.ucdavis.edu/training/documentation/.
The course will include experimental data organization, basic command line and high performance computing concepts, how to install software, use help, run applications, and the basics of building scripts and pipelines. Also covered will be basic R programming, working with data tables and generating figures, basic statistical concepts, and statistical model building.
UNIX/COMMAND LINE CONCEPTS
- Introductory materials, Unix/bash command line basics.
- Environment variables, your bash profile
- Basic bash shell scripting.
- Introduction to cluster computing
- Basics of git
- Folder and experiment structure
- Installation and running of simple sequencing tools.
- Constructing and run a simple bioinformatics pipeline.
R/DATA PROGRAMMING CONCEPTS
- Introduction to the R programming language.
- R markdown and notebooks.
- Constructing metadata tables, data munging, excel to R
- Basics of the tidyverse, data frame manipulation (join/rename/pipes)
- Figures in R, ggplot2
- Statistical concepts and model building