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Describe the goals of the changes to the analysis module.
The goal of this issue is to add an exploratory notebook to look at SingleR results from classifying NB samples using the NBAtlas reference. This notebook should contain at least:
The SingleR heatmap of assigned cell types
Maybe a delta median plot
A comparison between consensus cell types and SingleR cell types, using a heatmap colored by Jaccard similarity
A UMAP, because we must
Validation of SingleR cell types with marker genes
I'm frankly still back and forth for whether we're better served with a template notebook to look at results for individual samples, vs an overall notebook to look at all samples at once. I will want to look at one set of results first to help me make this decision, but I think in the end we may indeed want a small notebook to look at individual samples, and a larger notebook to perform more validation and comparison with consensus. Therefore additional comments will be added to this issue, and/or sub-issues may be broken out, to accomplish all this.
What will your pull request contain?
Notebook for exploring SingleR results
Will you require additional software beyond what is already in the analysis module?
No
Will you require different computational resources beyond what the analysis module already uses?
No
If known, when do you expect to file the pull request?
No response
The text was updated successfully, but these errors were encountered:
If you are filing this issue based on a specific GitHub Discussion, please link to the relevant Discussion.
Part of #1151
Describe the goals of the changes to the analysis module.
The goal of this issue is to add an exploratory notebook to look at
SingleR
results from classifying NB samples using theNBAtlas
reference. This notebook should contain at least:SingleR
heatmap of assigned cell typesSingleR
cell types, using a heatmap colored by Jaccard similaritySingleR
cell types with marker genesI'm frankly still back and forth for whether we're better served with a template notebook to look at results for individual samples, vs an overall notebook to look at all samples at once. I will want to look at one set of results first to help me make this decision, but I think in the end we may indeed want a small notebook to look at individual samples, and a larger notebook to perform more validation and comparison with consensus. Therefore additional comments will be added to this issue, and/or sub-issues may be broken out, to accomplish all this.
What will your pull request contain?
Notebook for exploring
SingleR
resultsWill you require additional software beyond what is already in the analysis module?
No
Will you require different computational resources beyond what the analysis module already uses?
No
If known, when do you expect to file the pull request?
No response
The text was updated successfully, but these errors were encountered: