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PCNE v2.0.0

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@riccabolla riccabolla released this 20 Aug 12:27
· 45 commits to main since this release
v2.0.0
d602c09

This is a major feature release, including new scripts, new features, and the removal of others.
The GC correction engine has been reworked to use a more robust LOESS-based model, and new features have been added to support batch processing and comparative analysis.

GC correction (#2 )

  • The LOESS smoothness is now estimated for each dataset using 5-fold cross-validation

Batch analysis

  • pcne_summary and PCNE_summary.R: allow summary of all pcne results. Useful when running on multiple isolates

Removed features

  • Single-copy gene feature has been removed due to its limited utility, and not clear advantages proofed (#3 ). Moreover, its removal should fix an issue when trying installation on mac (#4)

Other

  • Readme has been updated, providing a more complete explanation of all features (#1 )
  • Printed output has been simplified
  • --gc-plot now does not require an explicit filename.
  • Script's organization has been simplified, merging PCNE.R and GC_Correction.R into a single script named PCNE_analysis.R
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