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Draft of cell type section #63

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merged 8 commits into from
Mar 4, 2024
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allyhawkins
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Closes #30

Here I turned the outline in #60 into actual text. The biggest thing I'm unsure of is the first paragraph. Is this content what we're looking for regarding explaining why cell types? Or are there things missing?

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@jaclyn-taroni I addressed the remaining TODO's here, adding in the reference for the SingleR delta median calculation and updating the wording to not use reliable when talking about the CellAssign metric. Let me know what you think of the updated wording and if this clears up your question about what we mean be reliable labels.

Base automatically changed from allyhawkins/outline-celltype-results to main March 4, 2024 18:19
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github-actions bot commented Mar 4, 2024

Click the link below to download the manuscript build as a ZIP file.
This build is associated with commit b64d813.

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Let's keep it moving :sonic:

content/03.results.md Outdated Show resolved Hide resolved
Comment on lines +223 to +224
<!-- TODO: What exactly do we mean by reliable labels? Labels that are appropriate for the dataset -->
These values range from 0 to 1, with larger values indicating greater confidence in a given cell type label, so we expect more confident labels to have most values close to 1.
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This is still not quite right, in my opinion, but we can sort it out later.

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Okay, leaving in the TODO statement in case others have thoughts when we are reviewing everything.

Co-authored-by: Jaclyn Taroni <[email protected]>
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github-actions bot commented Mar 4, 2024

Click the link below to download the manuscript build as a ZIP file.
This build is associated with commit 632cd66.

Manuscript build

@allyhawkins allyhawkins merged commit cb2e516 into main Mar 4, 2024
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@allyhawkins allyhawkins deleted the allyhawkins/draft-cell-types branch March 4, 2024 19:40
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Draft: Results - cell type annotation
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