GEN220_2023

2023 Class

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Project maintained by biodataprog Hosted on GitHub Pages — Theme by mattgraham

GEN220: Highthroughput Biological Data Analysis - Fall 2023

See the Syllabus PDF for an overview of lecture topics.

Examples worked during class will be uploaded in this working repository. To check it out and keep it update.

git clone https://github.com/biodataprog/GEN220_2023_examples.git
cd GEN220_2023_examples
# ... time passes, new examples are uploaded
git pull # to get the latest version of the files

# let's also checkout the example datasets for the class
cd ..
git clone https://github.com/biodataprog/GEN220_data.git

Resources

• HPCC instructions on using SSH keys
• Access HPCC via web
• Github workflows and Software Carpentry Github Tutorial
• Software Carpentry UNIX/Shell Novice Tutorial
• UNIX command reference 1
• UNIX command reference 2
• Shell Scripting Tutorial
• Intro to Command-Line from HPCC

Major Topic Areas

• UNIX Shell scripting and using HPCC
• Python Programming
• Bioinformatics analysis methods
• Editors
  • VIM/VI
  • Nano
  • Emacs
  • Emacs Manual
  • Visual Studio - see HPCC INSTRUCTIONS - there is also a web-version you can run if you only have a tablet, the HPCC instructions will help set this up too.

Homework

• HW1 - Intro PDF
• HW2 - Airports PDF
• HW3 - Table Seating and Scattergories PDF
• HW4
• HW5

Project

• Project Team Ideas PDF
• Project Team Report Template PDF
• Project Presentation Info PDF

Lectures

The course will be divided into three topic areas.

UNIX

1. Course Intro / UNIX I: Cmdline PDF
2. UNIX: Running Tools PDF
3. UNIX: Analysis and Programming PDF
4. UNIX: Misc Tricks PDF

Python

1. Python: Intro PDF
2. Python: Logic,Loops,IO PDF
3. Python: Dictionaries and Functions PDF
4. Python: Workshop PDF
5. Python: Regular Expressions PDF
6. Python: Packages/BioPython PDF

Bioinformatics and Genomics

1. Bioinformatics: Basics and BLAST PDF
2. Bioinformatics: Short Reads PDF
3. Bioinformatics: RNASeq PDF
4. Bioinformatics: Microbiome PDF
5. Bioinformatics: Variation and SNPs PDF
6. Bioinformatics: Data Ranges PDF
7. Phylogeny and Gene Families PDF
8. Bioinformatics: Protein domains PDF
9. Bioinformatics: Orthology PDF
10. Bioinformatics: Genome Browsers PDF
11. Bioinformatics: Workshop - parsing data PDF

Other skills and Tools

1. Data viz with R PDF
2. R basics - Rstudio on HPCC http://rstudio.hpcc.ucr.edu, https://rstudio.cloud/ or install Rstudio on your own computer.
   • Also see Data Carpentry DataViz
3. Building Websites using github.io PDF