Material swap: Setup content

AlexsLemonade / training-modules

A collection of modules that are combined into 1-5 day workshops on computational topics for the childhood cancer research community.

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Material swap: Setup content #679

Closed sjspielman closed 1 year ago

sjspielman commented 1 year ago

As we head into May 2023's intro scRNAseq workshop, we're rearranging some topics. We'll be moving the pathway analysis day to advanced, and moving the cell typing to intro.

For this issue, address the following items:

[ ] Move relevant setup/ code between intro/advanced
[ ] Update setup link to new location: https://github.com/AlexsLemonade/training-modules/blob/3f438fe5d497efc45af5f0ebda08fef5e15b909e/scRNA-seq/06-overrepresentation_analysis.Rmd#L82
[ ] Update setup/magic-files.md to include files that may be needed for helping users during training.

jashapiro commented 1 year ago

Noting that one setup file that might be easy to miss is the normalized glioblastoma data for the cell typing exercise, which was originally produced by scRNA-seq-advanced/01-read_filter_normalize_scRNA.Rmd. It may be a bit wonky, but maybe we have the setup script in scRNA-seq run that notebook and then move the output file to reduce redundancy?

jashapiro commented 1 year ago

Adding note about future locations for links to work: scRNA-seq/setup/mouse-liver/prepare_mouse_liver_markers.Rmd should move to scRNA-seq-advanced/setup/mouse-liver/prepare_mouse_liver_markers.Rmd. If it moves somewhere else, we will need to update an exercise notebook: see https://github.com/AlexsLemonade/exercise-notebook-answers/pull/170#discussion_r1153450802