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Applied Genomics
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Course
Overview
Week 1
Introduction
GitHub Account
Lab
Intro to Unix
Lab
Week 2
Reproducible Research
Documentation
Version Control Systems
Data analysis with Unix
Lab
Week 3
Introduction to Snakemake
Intro to Snakemake
Lab
Week 4
Overview
Transcriptomics
nf-core
The Golden Snidget
Lab
Week 5
Week 6
COSMIC and Galaxy
Lab
Week 7
ChIP-Seq Pre-lab
Downstream ChIP-seq Analysis
Lab
Week 8
ATAC-Seq Data Analysis
Lab
Project Guidelines
Slides
Introduction
An Introduction to Unix
Reproducible Research
Unix Data Analysis
Snakemake
Databases
Epigenomics
ChIP-SEQ
Reference
Conda
misc
VS Code Alternatives
scRNA-Seq
UCSC Genome Browser
UCSC Xena Browser
nf-core chipseq
Readings
Resources
Scripting
Sysbio
AI Bot
GitHub
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Scripting
Scripting
See
The Art of Bioinformatics Scripting
Chapter 2 (Pages
13-18
)