• EMBL-EBI Training
  • On-demand training
  • Course materials
  • Single-cell RNA-seq analysis using R
My learning
My playlists
My account
Contact us
Logout
  • Login
  • Register

Single-cell RNA-seq analysis using R

  • Overview
  • Search
  • Course content
  • Planning the experiment
    • Keynote: Cellular heterogeneity in liver and drivers of disease
    • Droplet-based library generation overview
    • Pipeline overview
    • Experimental design
  • Processing data
    • Getting set up: infrastructure terms
    • Raw reads to expression matrix
    • Cell atlases & interpretation
  • Analysing data
    • Designing your analysis
    • Pre-processing and dimensionality reduction
    • From UMAP to annotation
    • Online tools and follow-up
  • Technical help sheets
  • Trainers biographies
  • Further learning
  • Your feedback

Creative Commons

All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.

Share with:

  • twitter
  • facebook
  • linkedin

Raw reads to expression matrix

Trainers: Iguaracy Pinheiro de Sousa and Daniel O’Hanlon

Overview: This session will focus on how to perform the initial alignment of the raw reads to the genome, to get an Expression Matrix (EM) in the end.

Materials:

Presentation slides

Practical:

Tutorial

Tutorial screencast:

Repository

Data

  • page navigation-left-circle-1_1 Getting set up: infrastructure terms
  • pageCell atlases & interpretation navigation-right-circle-1_1