Writing Reports
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
Table of contents
Learning Objectives
Writing Reports
Learning Objectives
Learning Objectives:
Use Quarto to write up your final project report
23
Functional Interpretation
24
Writing documents in Quarto