R Programming and RNA-Seq Analysis

Each of our lessons are recorded, to allow you to look back at the confusing parts and review anything you need to. Please contact any one of the admins for a link to the DataCamp course.

Download the  syllabus HERE
GitHub repository: HERE

To get started:

1. Download the entire github repository: here 

2. Unzip the download folder

3. For every week (except 1, 10, and 12), open the corresponding .Rproj file (if it exists) in RStudio to see the scripts/data for that week.

Week 1: Orientation

Here we go over the basics of R, RStudio, and Data structures in R. You can use the format here to work through the problems in RStudio.

Lecturer: Henry Miller

Homework

  1. Download R & RStudio

  2. Introductory R course in DataCamp: link

Week 2: Conditional logic and Control Flow

Lecturer: Paulino Ramirez

Homework:

  1. Intermediate R course in DataCamp

  2. Importing flat files chapter in DataCamp

  3. R assessment in DataCamp

  4. Week two practice problems

Week 3: Review 

Lecturer: Henry Miller

You can use the format here to go through the lesson in RStudio.

Homework

  1. Introduction to the Tidyverse in DataCamp

Week 4: The Tidyverse

Lecturer: Henry Miller

Homework

  1. Week 4 practice problems

  2. Continue practicing on Datacamp

Week 5: R for biological data science-how to use R to organize your big data

Lecturer: Henry Miller

GitHub directory: here

Homework

  1. Analyze qPCR data (found in project file link above) using R

  2. Continue practicing on DataCamp

Week 6: Starting Downstream RNASeq analysis with R

Lecturer: Dr. Yidong Chen

Homework

  1. Differential gene expression analysis with “airway” data set

Week 7: RNA Seq Visualization

Lecturer: Dr. Evelien Bunnik

Nice gg plot script

ERP010786.rda file

Homework

  1. EDA and DEG plots with airway data set

Week 8: Biological interpretation

Lecturer: Henry Miller

Week 9: Databases and Web-based analysis tools

Lecturer: : Paulino Ramirez & Henry Miller

Homework

  1. Gather data from Recount2 and analyze using previous methods along with web-based tools (e.g., enrichr).

  2. Complete the introduction to Shell course in DataCamp

Upstream RNA-Seq analysis with Linux shell:

Week 10: Linux shell basics

Lecturer:  Bernard Fongang, PhD

Homework

  1. Finish the Introduction to Shell course in DataCamp and download fastq files

Week 11: Alignment and read quantification

Lecturer: Chris Chiu, PhD

Week 12: Beyond gene expression

Lecturer: Siyuan Zheng, PhD