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Single cell RNA-seq analysis using Python

  • Overview
  • Search
  • Course Content
  • Planing your experiment
    • Wet-lab overview 
    • Dry-lab overview
    • Experimental design
  • Processing data
    • Raw reads to expression matrix
    • QC, pre-processing and normalisation
    • Single cell Expression Atlas and single cell data submission
  • Analysing data
    • Designing your analysis
    • Dimensionality reduction, clustering, and annotation
    • Batch correction and data integration
    • Spatial transcriptomics
    • Abundance and differential expression
  • Technical help sheet
  • Trainer biographies
  • Further learning
  • Your feedback

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Raw reads to expression matrix

Trainers: Jiawei Wang and Jinzheng Ren

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 for cellranger
  • Main presentation slides

Practical

  • GitHub repository
  • page navigation-left-circle-1_1 Processing data
  • pageQC, pre-processing and normalisation navigation-right-circle-1_1