Bioinformatics Workshops

2018 Bioinformatics Summer Workshop Materials

Go to our lab's YouTube channel. There you will find some short videos on Linux that were recorded as part of last year's workshop series. These are a good resource to get familiar with the subjects that we will cover. If you do not already have Linux installed on your machine, the first video in the series will walk you through the steps of downloading and installing Linux as a VirtualBox on your Mac or PC.

• • Day 1: Commands

  • Days 2 and 3: Commands

  • Day 4: Commands

  • Day 5: Commands

2017 Bioinformatics Summer Workshop Materials

Linux Workshop links:

• • Module 0 : Installing Ubuntu On Virtual Box (YouTube)

  • Module 1 : Linux GUI (YouTube)

  • Module 2 : Linux Terminal Basics (YouTube)

  • Module 3: Working With Files (YouTube)

  • Module 4: Editing Files With vi (YouTube)

  • Module 5: Remote Access And File Transfer (ssh/scp/sftp) (YouTube)

  • If you do not have access to a Linux based machine, you may try these web-based Linux terminals: Coding Ground | Webminal

Programming in Perl (2017 Bioinformatics Summer Workshop)

Perl Workshop links:

• Module 1: Perl Basics (YouTube)

• Module 2: String Manipulation with Perl (YouTube)

• Module 3: If Statements (YouTube)

• Module 4: Loops (YouTube)

• Module 5: File I/O (YouTube)

• Session 1 (live presentation recorded): WebEx video | Supplementary Materials

• Session 2 (live presentation recorded): WebEx video | Supplementary Materials

• Session 3 (live presentation recorded): WebEx video | Supplementary Materials

• Session 4 (live presentation recorded): WebEx video | Supplementary Materials

• Session 5 (live presentation recorded): WebEx video | Supplementary Materials

Basic Programming in Python (2018 Bioinformatics Summer Workshop)

Before the workshop begins you should ensure that you have some way of running Python on your machine. You have many options! The first of which is the website: https://repl.it/ . This site will let you code in a variety of languages (including Python) and execute alongside your code.

For those of you that will want to code “offline,” you can follow the installation guides on https://www.python.org/ for your specific operating system.

Either option will work for the scope of this workshop! Questions? Contact Casey Cole, coleca@email.sc.edu.

Introductory Data Analysis in R (2018 Bioinformatics Summer Workshop)

Before the workshop begins you should ensure that you have some way of running R on your machine. For those of you that do not have R installed, here is a link to the website: https://www.r-project.org/

• • Day 1: Code | Dataset

  • Day 2: Code

  • Day 3: Code

  • Day 4: Code

  • Day 5: Code

  • Additional files: FASTQ file | aliveCounts.txt | deadCounts.txt | Genes.txt

• Session 4 (live presentation recorded)

2017 Bioinformatics Summer Workshop

R Workshop links (2017 Bioinformatics Summer Workshop):

• Session 1 (live presentation recorded): WebEx video

• Session 2 (live presentation recorded): WebEx video | Supplementary Materials

• Session 3 (live presentation recorded): WebEx video | Supplementary Materials

• Session 4 (live presentation recorded)