GEN220_2020

2020 Edition of the Class

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

GEN220: Highthroughput Biological Data Analysis - Fall 2020

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_2020_examples.git
cd GEN220_2020_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

Homework

Project

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: Variation and SNPs PDF
  5. Bioinformatics: Data Ranges PDF
  6. Bioinformatics: Protein domains PDF
  7. Bioinformatics: Orthology PDF
  8. Bioinformatics: Genome Browsers PDF
  9. Bioinformatics: Workshop - parsing data PDF
  10. Odds and Ends PDF

Other skills and Tools

  1. R basics - Rstudio on HPCC http://rstudio.hpcc.ucr.edu, https://rstudio.cloud/ or install Rstudio on your own computer.
  2. Building Websites using github.io PDF