Instructor Notes
This is a placeholder file. Please add content here.
Spatially Resolved Transcriptomics in Life Sciences Research
Data and Study Design
Data Preprocessing
Instructor Note
If the data does not load in correctly, verify that the students used the mode = “wb” argument in download.file() during the Setup. We have found that Windows users have to use this.
Remove Low-quality Spots
Instructor Note
You don’t have to have the students type out the next block. It may be better to let them focus on the concept rather than typing.
Instructor Note
There is no need to have students type out the figure titles and axis labels.
Instructor Note
There is no need to have students type out the figure titles and axis labels.
Normalization in Spatial Transcriptomics
Instructor Note
Don’t have the students type this. Show the plots and discuss them.
Feature Selection, Dimensionality Reduction, and Spot Clustering
Deconvolution in Spatial Transcriptomics
Differential Expression Testing
Putting it all Together
Instructor Note
In the next Challenge, you can assign a certain number of principal components and cluster resolution to each student or group of students and compare the clustering results.