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. Reading, navigating, and plotting data

    Lecture Slides Available Here

Bulk RNA sequence analysis (Day 3, Mon.)

  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 (Day 4, Tue. - Day 5, Wed.)

  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 (Day 6 - Thurs.)

  1. Spatial Transcriptomics

    Slides

Prior versions of the CRI Bioinformatics Bootcamp