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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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2024 June updates #773

Open sjspielman opened 5 months ago

sjspielman commented 5 months ago

This issue tracks changes we should implement as noticed during June 2024's Intro scRNA-seq training.

sjspielman commented 5 months ago

Looks like the R4DS booked has moved, we should update links: https://github.com/search?q=repo%3AAlexsLemonade%2Ftraining-modules%20r4ds&type=code

sjspielman commented 5 months ago

Too many spaces surrounding the comma at package , which: https://github.com/AlexsLemonade/training-modules/blob/31bf43141a5fc467be246a46dc101c006de2af5c/intro-to-R-tidyverse/03-intro_to_tidyverse.Rmd#L181

jashapiro commented 5 months ago

Apparently we may need to load the alevinQC package before running it. https://github.com/AlexsLemonade/training-modules/blob/31bf43141a5fc467be246a46dc101c006de2af5c/scRNA-seq/01-scRNA_quant_qc.Rmd#L234-L243

sjspielman commented 5 months ago

Just a thought as we make plots, should we use theme_set(theme_bw()) at the top of notebooks that make many plots?

jaclyn-taroni commented 5 months ago

Update this link to OSCA to use a current version of Bioconductor (3.19 at the moment):

https://github.com/AlexsLemonade/training-modules/blob/31bf43141a5fc467be246a46dc101c006de2af5c/scRNA-seq/05-clustering_markers_scRNA.Rmd#L190

jashapiro commented 5 months ago

Update this link to OSCA to use a current version of Bioconductor (3.19 at the moment):

https://github.com/AlexsLemonade/training-modules/blob/31bf43141a5fc467be246a46dc101c006de2af5c/scRNA-seq/05-clustering_markers_scRNA.Rmd#L190

All links to OSCA?

sjspielman commented 5 months ago

Cell type slides: We link review from 2021 about automated annotation tools, but 2021 is ages ago in single-cell time. Are there more recent papers we can reference here?