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Genomics Aotearoa: Single-Cell RNA-seq Analysis Workshop

May 9, 2024 @ 9:00 am – 1:00 pm
Tyler McInnes

This workshop, taught by Professor Mik Black, will introduce skills and tools required for the analysis of single-cell RNA-seq data (scRNA-seq data) in R. The workshop will be taught online over four half-days, on May 8th, 9th, 15th and 16th  (9am – 1pm). You should attend all 4 sessions.

This is an advanced workshop which requires an intermediate level of R knowledge and experience. To participate in this workshop you must have either completed the Genomics Aotearoa Intermediate R workshop, or have an equivalent level of experience (e.g., be a semi-regular R user). Because of the complexity of this workshop we will not have the time or resources to solve coding errors. However, the focus of this workshop will be on the concepts and discussion of the statistical methodology rather than your ability to code quickly.

Because we expect a high level of interest in this workshop and we have limited spaces, we are inviting expressions of interest no later than Friday April 26th and will select a group of attendees based on needs and experience. We will endeavour to maximise the overall positive impact on research in Aotearoa and distribute this training as fairly as possible. You will be advised whether you are able to attend the training by end of day Monday April 29th

If we are not able to offer you a space in this training, you will be kept informed about future options for scRNA-seq training.

What will this workshop cover?

  • Alignment and feature counting with Cell Ranger (briefly).
  • QC and exploratory analysis.
  • Normalisation.
  • Sctransform: Variant Stabilising transformation.
  • Feature selection and dimensionality reduction.
  • Batch correction and data set integration.
  • Clustering.
  • Identification of cluster marker genes.
  • Differential gene expression analysis.
  • Differential abundance.

*Note that some of this material may be mentioned only briefly due to time constraints, in which case you will be pointed towards supplementary material for self-guided learning.

If you have any questions about this workshop, please contact Genomics Aotearoa Training Coordinator Dr Tyler McInnes (

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