Course overview

R Workshop (Day 1, Sat. - Day 2, Sun.)

1. Introduction to R

2. Basic plotting and statistics

3. Clustering concepts and correlation

4. Common challenges and additional resources

Bulk RNA sequence analysis (Day 3, Mon.)

• Introduction to DNA and RNA sequencing lecture slides (Obi Griffith and Malachi Griffith)

1. Introduction to rnabio.org and bulk RNAseq dataset (Lead: Obi/Malachi)

2. Introduction to IGV (Lead: Malachi)

3. Differential Expression Analysis (DESeq2) (Lead: Zach) Code blocks for DE

4. Differential Expression Visualization (DESeq2) (Lead: Zach)

5. Differential Expression Visualization (Advanced R) (Lead: Obi/Charles)

6. Pathway Analysis (Lead: Obi)

7. Batch Correction (Lead: Malachi)

Single cell RNA sequencing (Day 4, Tue. - Day 5, Wed.)

• Introduction to scRNA sequencing technology lecture slides (Obi Griffith)
• Introduction to scRNA sequencing analysis lecture slides (Malachi Griffith)

1. Introduction to scRNAseq dataset (Lead: Malachi)

2. QA/QC and Clustering (Lead: Evelyn)

3. Cell Type Annotation (Lead: Kelsy)

4. Differential Expression (Lead: Kartik)

5. Gene Set Enrichment (Lead: Kartik)

6. Cancer Cell Identification (Lead: Kartik)

7. Trajectory Analysis (Lead: Evelyn/Malachi)

8. TCR/BCR Repertoire Analysis (Lead: Obi)

Imaging (Day 6, Thu.)

1. Intro to Python

2. Spatial Analysis