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Update scRNA-seq chapter and add a paragraph on quantification of gene expression #371

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Merged
merged 41 commits into from
May 19, 2025

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LuisHeinzlmeier
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@LuisHeinzlmeier LuisHeinzlmeier commented May 12, 2025

@LuisHeinzlmeier LuisHeinzlmeier linked an issue May 12, 2025 that may be closed by this pull request
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This is much better and I really like what you're doing here. This is great work already!

  1. It's a bit dangerous to talk so much about the central dogma because everyone knows that it's limited and does not paint the whole picture. A biologist will notice this while reading :)
  2. Nit: You missed a few new lines for sentences.
  3. I know that it's annoying work but I think we can link to a few more existing glossary items in a few places to make some things clearer. I trust your judgement.

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Thank you very much for the feedback! Should I convert the .md to an .ipynb to be able to render the questions?

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Zethson commented May 15, 2025

If necessary, yes. @seohyonkim ?

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Yes, to use the quiz feature, you would have to use .ipynb!

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@LuisHeinzlmeier LuisHeinzlmeier changed the title Still in progress! Update scRNA-seq. Update scRNA-seq and add a paragraph on quantification of gene expression May 19, 2025
@LuisHeinzlmeier LuisHeinzlmeier changed the title Update scRNA-seq and add a paragraph on quantification of gene expression Update scRNA-seq chapter and add a paragraph on quantification of gene expression May 19, 2025
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Thank you very much for the feedback!

  1. Avoided using the term central dogma that often. Also, read this short article based on your comment. Thank you for drawing attention to this 💪

  2. Added a couple of new lines.

  3. Added mRNA and sequencing to the glossary and linked the terms in most chapters (at least in those we have already worked through).

@LuisHeinzlmeier LuisHeinzlmeier requested a review from Zethson May 19, 2025 17:34
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Thank you!

More details on this computational process will be described in the next chapter.

Ideally that would be a sphinx link.

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Thank you!

More details on this computational process will be described in the next chapter.

Ideally that would be a sphinx link.

Added a link to the next chapter.
I think then it is ready to be merged from my side! 🚀

@Zethson Zethson merged commit 08886ad into main May 19, 2025
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@Zethson Zethson deleted the updates_scRNA_chapter branch May 20, 2025 19:35
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Add mRNA to glossary Adding tables + improve structure of strengths and limitations
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