These are resources to help students interested in developing foundational skills useful for computational biology. The basic section contains short introductions, and advanced resources are more complete references.

Basic resources and introductions

Git and GitHub. Git can feel overwhelming, but just dive in and it will be worth your time.
Markdown. Markdown is an easy-to-read, easy-to-write plain text format.
R and Bioconductor. R is unparalleled for statistical packages and powerful data visualization.
- Learn R Programming intro to R.
- Bioconductor for Genomic Data Science (Watch the first 4 lectures, about 25 minutes of video)
- Swirl Interactive platform for learning R
Unix command line.
- Matt Might’s basic guide to Unix
YAML
- Learn YAML in 5 minutes

Advanced resources and complete references

Git and GitHub
- Resources for learning git
- Setting up authorized SSH keys with github
- Writing good commit messages (Read after you’ve used git for awhile)
- ProGit
- ProGit on version control
- GitHub Cheatsheet
Markdown
- Markdown Original Specification (and that site in markdown)
- Github Flavored Markdown
- Markdown Cheatsheet
R
- An introduction to R - all-purpose intro from the R Foundation
- Advanced R - Wickam’s free online book on R in general
- data.table cheat sheet
- Matt Dowle’s data.table talk - describes motivation for creating data.table.
- R cookbook - ggplot recipes
- Coursera R Programming course - R programming course including instructional videos
- ggplot2 cheatsheet
Bioconductor
- Kasper Hansen’s course, Bioconductor for Genomic Data Science (about 6 hours of video)
- Reference card
- Stuff from Laurent Gatto
- Website and material for CSAMA; for example, you can identify online course material at bioconductor’s course listing; some example courses: Intro to bioconductor, Machine Learning and Parallel Computing, RNA-seq
- Vignettes from GenomicRanges
- Vignettes from LOLA
Unix command line
- Bash guide for beginners
- Bash tutorial list
- Matt Might’s scupting text
- Matt Might’s settling in to unix
- Search for Unix command line tutorials
Python
- How to Think Like a Computer Scientist: Learning with Python
- Dive into python - a free online textbook.
- Pandas cheatsheet
Programming concepts
High-performance computing and SLURM. SLURM (the Simple Linux Utility for Resource Management) is the cluster workload manager used by Rivanna at UVA and at many high-performance clusters elsewhere. If you need to submit jobs to a cluster, learn SLURM.
- Introduction to Rivanna at UVA
- SLURM Quick Start Guide
- SLURM docs at Rivanna
- Rivanna environment modules gives you commands to load installed software into your linux environment
Visualization
- Fundamentals of Data Visualization - online book covering visualization elements and problem categories
Writing
- Duke Scientific Writing Resource
Writing R/Bioconductor packages
- Writing R packages - Wickam’s free online book on writing R packages
- Blog post on writing R packages - A gentle introduction to your first R package.
- Roxygen2 is the generally accepted method for documenting R packages
- Bioconductor Contributions
- BioC HowTo

Here’s a separate list of resources for bioinformatics at UVA. Other bioinformatics resources from Stephen Turner, and for workshops on these topics, check out bioconnector at UVA.