training-modules

scRNA-Seq Training Module

This CCDL-designed module covers the analysis of single-cell RNA-seq data using Salmon’s Alevin and scater/scran packages.

It depends on knowledge gained in the Intro to R and analyses are performed within a Docker container or on the CCDL RStudio server. It covers normalization and dimension reduction methods that can be used for both tag-based and full-length single-cell data, as well as the quantification of tag-based scRNA-seq data.

The notebooks that comprise this module are:

• Quantification of tag-based scRNA-seq data
• Quality control and filtering
• Normalization
• Dimension reduction
• Clustering
• Cell type annotation

Additional exercise notebooks:

• Quantification
• Clustering
• Cell type annotation

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