Computational Research

This section is meant to facilitate the sharing of useful tips for computational, bioinformatic, or plotting resources!

1. Getting Account on GHPCC Cluster

2. Organization and storage on the GHPCC Cluster

3. Using the GHPCC Cluster and general unix tips

4. Python tips

5. R/RStudio and R package tips

6. Mounting cluster directory

Useful tutorials and free courses in unix, python, and R:

Unix

• • Software Carpentry's Unix Shell Core Lesson

  • UNIX Tutorial for Beginners

R & ggplot2:

• • Software Carpentry's Programming with R Core Lesson

  • Software Carpentry's R for Reproducible Scientific Analysis Core Lesson

  • A Beginner's Guide to Using R

  • Interactive R instruction with swirl (within RStudio)

  • Datacamp Introduction to R

  • A set of R lessons compiled by previous UMass students

  • Setting working directories and file paths in R

  • Basics of R studio, help functions, assignment, naming conventions, norms

  • Basic data types/structures in R

  • Set-by-step intro into the usage of ggplot2

  • Breakdown of ggplot2 synthax

  • Gallery of plots that can be made in R

  • Reference list of all ggplot plots & aesthetics + details

Python

• Learn Python

  • Software Carpentry's Programming with Python Core Lesson

  • Software Carpentry's Plotting and Programming with Python Core Lesson (note, this is an alternative basic lesson, not really about plotting)

  • Test your python skills with simple tasks in the Rosalind Python Village

Primers on Computational Biology from PLOS Comp Bio