VIBS-689 Special Topics in Single Cell Analyses

VIBS-689 Special Topics in Single Cell Analyses, Summer'19

Instructor: James Cai (

Teaching Assistant: Daniel Osorio (

Lectures: Tue & Thr 2:00 - 3:15 PM, VMR (bldg 1811) Rm 378

Office hours: Wed 10-12, VMR (bldg 1811) Rm 384

Description of Course

Single cell technologies have made genomic analysis on the single cell level more accessible than ever. Recent development of these technologies, especially single-cell RNA-seq (scRNA-seq), has revolutionized genomic research. This course focuses on the computational biology of scRNA-seq analysis.


  1. Introduction to single cell technologies (C1 and 10X) and programming basics (Matlab/R) for single cell analyses (7/2 Tue)
  2. Getting counts by cell (10X cell-ranger and salmon-alevin pipeline) and QC (7/3 Wed or 7/5 Fri)
  3. Data normalization and imputation (7/9 Tue)
  4. Data visualization (PCA, tSNE and PHATE) (7/11 Thr)
  5. Clustering analysis and cell type identification (7/16 Tue)
  6. Feature selection for identifying highly variable genes (7/18 Thr)
  7. Differential expression analyses with scRNA-seq and bulk RNA-seq data (7/23 Tue)
  8. Trajectory analysis (7/25 Thr)
  9. Manifold alignment and coupled nonnegative matrix factorization for combining different types of data, e.g., scRNA-seq and scATAC-seq (7/30 Tue)
  10. Construction of regulatory network using scRNA-seq data (8/1 Thr)
  11. Final exam (8/6 Tue)

Class Notes and Resource Materials

Class notes are distributed in class. There is no required textbook.

Additional readings: You are responsible for additional readings that will be announced in class.