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Normalisation and bug fixes #39

Merged
merged 2 commits into from
Feb 25, 2024
Merged

Normalisation and bug fixes #39

merged 2 commits into from
Feb 25, 2024

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maplesond
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Adding normalisation to the beginning of the comparison pipeline.

Also:

  • Essentiality analysis report now works correctly
  • Updating normalisation tool to output according to a defined directory structure
  • Updating call to pandas read CSV to avoid deprecation warning
  • Updating flowchart
  • Updating installation guide to include manual installation of EdgeR
  • Removing unnecessary essentiallity CSV file from output
  • Replacing deprecated pkg_resources call with importlib

Previously we were using the .all.csv as input to the essentiality report file, however this expect the .tsv input from the insertion site analysis output.  This fix changes that.

Also we remove the .all.csv file from output generated by the R script as it doesn't serve any purpose.

Also updated the docs.

fixing stuff
…peline

We add normalisation to the beginning of the plot compare pipeline.

fix no normalisation issue
@maplesond maplesond merged commit 5e47b2e into master Feb 25, 2024
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2 participants