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Add tb validation notebook #4

Merged
merged 18 commits into from
Jul 29, 2024
Merged

Add tb validation notebook #4

merged 18 commits into from
Jul 29, 2024

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ryanjameskennedy
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@ryanjameskennedy ryanjameskennedy commented Jun 25, 2024 •
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Added

  • Added tb validation notebook
  • Added output csv for failed validation samples
  • Added differential matrix for validation
  • Added saureus validation notebook
  • Added --generate_matrix argument to cli
  • Added alter_sample_id filter
  • Added summed differential matrix
  • Added mean coverage plot
  • Added jitter to mean coverage boxplot

Fixed

  • Fixed pyproject.toml setuptools bug
  • Fixed cgmlst comparison and plots
  • Fixed fix subarg
  • Fixed TN/TP/FN/FP plots

Changed

  • Changed id format for fix and missing
  • Changed matrix to boxplot, jitter, and annotate

@ryanjameskennedy ryanjameskennedy force-pushed the add-validation-notebook branch from 2df1740 to ee99781 Compare June 26, 2024 06:20
@ryanjameskennedy ryanjameskennedy requested a review from mhkc July 12, 2024 13:04
@ryanjameskennedy ryanjameskennedy merged commit 851ab88 into master Jul 29, 2024
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@ryanjameskennedy ryanjameskennedy deleted the add-validation-notebook branch July 29, 2024 14:50
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@mhkc mhkc Awaiting requested review from mhkc

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