Course overview

R Workshop (1.5 Days, Saturday-Sunday)

1. Introduction to R

2. Basic plotting and statistics

3. Clustering concepts and correlation

4. Reading, navigating, and plotting data

   Lecture Slides Available Here

Bulk RNA sequence analysis (1.5 Days, Sunday-Monday)

• 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: Malachi)

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

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

6. Pathway Analysis (Lead: Obi)

7. Batch Correction - brief introduction (Lead: Malachi)

Single cell RNA sequencing (1.5 Days, Tuesday-Wednesday)

• 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)

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

Spatial Transcriptomics (1.5 Days, Wednesday-Thursday)

1. Spatial Transcriptomics

   Slides

Prior versions of the CRI Bioinformatics Bootcamp

• 2024