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Speed up nest and unnest for massive datasets in tidySingleCellExperiment #70

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stemangiola opened this issue Jul 19, 2023 · 3 comments
Open

Speed up nest and unnest for massive datasets in tidySingleCellExperiment #70

stemangiola opened this issue Jul 19, 2023 · 3 comments
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enhancement New feature or request

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@stemangiola
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There is an example in the tidyseurat repository of how we can speed out nesting for very simple use cases using the split and merge functionality of Surat
@stemangiola stemangiola added the enhancement New feature or request label Jul 19, 2023
@stemangiola stemangiola changed the title Speed up nesting and unnesting for massive datasets Speed up nesting and unnesting for massive datasets in tidySingleCellExperiment Jul 19, 2023
@stemangiola stemangiola added good first issue Good for newcomers and removed good first issue Good for newcomers labels Jul 21, 2023
@stemangiola stemangiola changed the title Speed up nesting and unnesting for massive datasets in tidySingleCellExperiment Speed up nest and unnest for massive datasets in tidySingleCellExperiment Jul 28, 2023
@stemangiola
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@LiNk-NY this is one of the challenges I was mentioning.

@william-hutchison
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Hello, I would be happy to have a go at solving this.

@william-hutchison william-hutchison self-assigned this Aug 9, 2023
@william-hutchison
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I have been able to considerably speed up nesting of a single column by using SingleCellExperiment's [] subsetting, but find my nested objects don't always cleanly unnest.

I will keep working at this, but if anyone else would like to have a go feel free! The changes I have made are available here for reference: https://github.com/william-hutchison/tidySingleCellExperiment/tree/master.

@stemangiola stemangiola moved this to In Progress in tidyomics open challenges Aug 15, 2023
@stemangiola stemangiola moved this from In Progress to Todo in tidyomics open challenges Aug 23, 2023
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@stemangiola @william-hutchison