Intro to Linux and Bash
References
ISG 5311 - Genomic Data Analysis in Practice
Preface
Intro to Linux and Bash
1
Getting Connected
2
Getting Started with Linux
3
Working with Files
References
HPC and SLURM
4
Scripts and putting it all together
5
SLURM: the job scheduler
6
Data Storage and Software on HPC
7
Bonus: Making it easier to log in to the cluster
8
Bonus: Customizing your shell
Sequencing Data
9
High-throughput sequencing data
10
Sequencing platforms
11
Sequence QC
Measuring Gene Expression I
12
Overview of differential expression with RNA-seq
13
Project Organization
14
Retrieving data
15
Reference Alignment
16
Expression Quantification
Statistical Analysis I: R and RStudio
17
Getting to Know R and RStudio
18
Base R with Swirl
19
R and the Tidyverse
Statistical Analysis II: Differential expression analysis
20
Overview
21
Count Data
22
Differential Expression Analysis
23
Functional Interpretation
Writing Reports
24
Writing documents in Quarto
Intro to Linux and Bash
References
References
3
Working with Files
HPC and SLURM