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R workshop on single cell genomics at BC Cancer March 2019
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using-r-bioconductor-bccancer-march-19.Rmd

README.md

R Single-Cell Workshop, BC Cancer 2019

Workshop details: March 26th 2019 12pm - BCCRC Diamond Family Theatre

This workshop will cover the following:

  1. Read 10X single-cell RNA-seq data into SingleCellExperiment objects
  2. Know how to navigate SingleCellExperiment objects
  3. Basic QC of single-cell RNA-seq data using scater
  4. Create low dimensional plots (PCA, UMAP, tSNE)
  5. Assign cells to known cell types using cellassign

What do to beforehand

You must have R, RStudio, and git installed for this workshop. Then:

  1. Clone this repo
git clone https://github.com/kieranrcampbell/r-workshop-march-2019.git
  1. Open the RMarkdown file using-r-bioconductor-bccancer-march-19.Rmd

  2. Make sure the required packages are installed (see section "Required Packages")

  3. Install cellassign (see section "Installation of cellassign")

If you have problems please file a github issue.

Tutorial materials

The RMarkdown document compiled as html can be found here.

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