Please provide some background on the proposed additions or changes.
After we initiate the merge SCE script in #332, we will want to account for batch effects, identify the highly variable genes, and perform dimensionality reduction on the merged SCE object.
What are the changes that you are proposing?
After merge the list of processed SCE objects, we will want to add steps to do the following with the merged object:
account for batch effects
identify the subset of highly variable genes
perform multi-batch PCA
perform UMAP
Please describe the proposed solution.
Similarly to what is done in the merge sces script in the scpca-nf repo, we will want to add the steps mentioned above to the data integration module's merge-sces.R script, after the step that performs the SCE object merging.
cbethell
commented
1 year ago
Please provide some background on the proposed additions or changes.
After we initiate the merge SCE script in #332, we will want to account for batch effects, identify the highly variable genes, and perform dimensionality reduction on the merged SCE object.
What are the changes that you are proposing?
After merge the list of processed SCE objects, we will want to add steps to do the following with the merged object:
Please describe the proposed solution.
Similarly to what is done in the merge sces script in the scpca-nf repo, we will want to add the steps mentioned above to the data integration module's merge-sces.R script, after the step that performs the SCE object merging.