Presenter: Dr. Jennifer Foltz
This homework builds on what we learned last week. To complete the homework assignment you will need to have R/Rstudio installed. You will not be able to open the Rmarkdown homeowrk file without this installation. In addition, we recommend installation of the following packages within R/Rstudio to do the homework for week 18 and week 19. (note: RStudio may prompt you to install these when you open the Rmarkdown file)
- Seurat
- RMarkdown
- ggplot2
- cowplot
- dplyr
- Matrix
- viridis
- NEW for day 2: harmony
- NEW for day 2: SeuratWrappers
- NEW for day 2: scCustomize
To run the day 2 Rmarkdown homework file, you will use the same dataset as last week- see last week's instructions. Make sure to install the 3 new packages listed above.
Use the #bfx-workshop slack channel to ask questions.
There are several questions in this week's notebook:
- Based on the above, how many PCs do you think are informative?
- Now we cluster using both the RNA and protein data. How does it compare to RNA only?
For-credit-students: send a brief answer to each question to John as proof of completion.