Analysis of single-cell RNA-seq data: Normalization, dimensionality reduction, clustering, and lineage inference
Fanny Perraudeau (@fperraudeau) Davide Risso (@drisso), and Kelly Street (@kstreet13)
This repository contains the code and data needed for the workshop.
The workshop is divided into five main parts:
- Pre-processing: scone
- Normalization and dimensionality reduction: zinbwave
- Cell clustering: clusterExperiment
- Cell lineage and pseudotime inference: slingshot
- Differential expression analysis along lineages
A very similar version of the workflow is available at https://f1000research.com/articles/6-1158/v1