Single-Cell Workshop 2014: RNA-seq

Computational Analysis

The hands-on session consists of several examples covering the typical steps involved in the analysis of single-cell RNA-seq datasets. Please follow the instructor the the sequence of exercises below


Quantify total signal associated with each gene by going from fastq that are typically produced by the sequencing facility to read counts for each gene in each cell.

Differential Expression

Read in and normalize the read counts for each gene/cell, and test for differential expression using different methods.

Subpopulation Analysis

Look for heterogeneity within the analyzed population of cells using different approaches.

Continuous Differences

Order cells within heterogeneous populations according to major or secondary axes of variation.

Gene Correlation Networks

Determine clusters of genes that tend to vary together within the measured cell population.