BioC 2017 workshop

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:

1. Pre-processing: scone
2. Normalization and dimensionality reduction: zinbwave
3. Cell clustering: clusterExperiment
4. Cell lineage and pseudotime inference: slingshot
5. Differential expression analysis along lineages

A very similar version of the workflow is available at https://f1000research.com/articles/6-1158/v1