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GEN220: High Throughput Biological Data Analysis
Home
UNIX
UNIX I: Logging In and Command Line Basics
UNIX II: Files, Data and Running Programs
UNIX III: Shell Programming
UNIX III Lab: Data Processing with Pipes
UNIX IV: Running Analyses on the Cluster
Python
Python I: Values, Variables and Strings
Python II: Decisions, Lists, Loops and Files
Python III: Dictionaries, Sets, Tuples and Functions
Python Workshop: Practice with Real Data
Python IV: Modules, Packages and Biopython
Python IV: Tables with Pandas
Python V: Regular Expressions
Python V: Regular Expressions Worked Examples
Plotting Data with Python
Bioinformatics
Basics and BLAST
Workshop: Parsing Data
Short Reads
Genomic Data Ranges
RNASeq
Variation and SNPs
Workshop: SNPs per Gene and Splice Sites
Protein Domains
Orthology
Workshop: Orthologs and Gene Networks
Phylogeny and Gene Families
Sequence Evolution and Statistics
Microbiome
Genome Browsers
Other Skills and Tools
Plotting with R and ggplot2
Building Websites
Tables: CSV, Parquet and SQL with DuckDB
Assignments
HW0 - Intro
HW1 - Unix
HW2 - Python 1
HW3 - Python and BLAST
HW4 - AI Programming
HW5 - GitHub Website
Project Topics
Project Team Ideas
Project Report Template
Project Presentation Info
Resources
Syllabus
Git and GitHub Guide
SSH Keys
Search GEN220: High Throughput Biological Data Analysis
Course repo on GitHub
Class examples
Resources
Syllabus
PDF
Git and GitHub guide
PDF
- setup, logging in (SSH keys, tokens, gh), recipes, cheat sheet
SSH keys
PDF
Table of contents
Syllabus
Git and GitHub Guide
SSH Keys