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      BIS 180L

Home
CLI
Introduction to the Command Line 1
Introduction to the Command Line 2
Introduction to the Command Line 3
Extra
BashCrawl
Challenge & Homework Solutions
Software Installation
Installation using make and cmake
Conda
Introduction to R
Introduction to R Day 1
Introduction to R Day 2
Introduction to R Day 3
Challenge solutions
Alignment
Local Alignment
Python
Intro
Basic Data Types
Flow Control, Functions, Files, Errors
Writing Programs
Biopython and bamnostic/pysam
Next Steps
Bioinformatics File Types
RNA-Seq
  Data Reduction
Files and Filetypes
Prepare dataset
Preprocessing raw data
Indexing a Genome
Alignment with Star
Generating counts tables
  Data Analysis
Prepare R for data analysis
Annotation from BioMart
Differential Expression Analysis
Pathway Analysis

Now what?

Topics we didn’t cover

Rosalind

Rosalind is a platform for learning bioinformatics programming. It has many bioinformatics programming exercises to tackle practicing how to code.

Practice, Practice, Practice

As with any skill, you need to practice! Try starting from the beginning of the course and trying everything from scratch. If you have an experiment you are working on right now, try coding some python to help you do some of the analysis. Feel free to contact me if you have any questions or run into any problems. Happy Coding!