GEN220_2022

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

GEN220: Highthroughput Biological Data Analysis - Fall 2022

See the Syllabus PDF for an overview of lecture topics.

We will use Piazza for discussions and Q&A.

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_2022_examples.git
cd GEN220_2022_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

• SSH keys
• 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

Homework

• HW1 - See canvas/piazza for github classroom link
• HW2 - Homework 2 PDF
• HW3 - Homework 3 PDF
• HW4 - Homework 4 PDF

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