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@amnona amnona released this 20 Jul 13:26
· 27 commits to master since this release
2020.8.6
8325d9c
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Learn about vigilant mode.

Incompatible changes:

  • Change random_seed to work with numpy.random.default_rng. This may cause different random numbers compared to the old versions using numpy.random.seed().
  • Change parameter names in some functions
  • Rename filter_abundance() to filter_sum(abundance)
  • Other backwards incompatible function API changes and code refactoring.

New features:

  • Add RatioExperiment for working with ratios between two groups of features
  • Add random_seed option to tranforming.permute_data()
  • Add bad_color parameter to heatmap() and derivative functions
  • Add more methods for MS1Experiment
  • Add q-values (correted p-values) to dsfdr and derivative functions. This is manifested in a new feature_metadata field ("qval") for results of diff_abundance() / correlation()
  • improved GUI for qt5 heatmap database enrichment results.
  • Add read_qiime2() function to enable reading of qiime2 feature tables artifacts with the associated representative sequences and taxonomy artifacts (without the need to install qiime2)
  • Add Experiment.validate().
  • Change default color scale in heatmap plot to linear scale for Experiment and log scale for AmpliconExperiment and MS1Experiment.
  • Move to pytest for unit tests and doctests.
  • Add new mechanism to register a function to a class as a method automatically. In order for a function to be registerred to a class, it must be a public function and has type hint of the class type for its first function parameter and return value.
  • Clean and improve API documentation.

Other changes:

  • make scikit-bio an optional dependency (needed only when processing dendrograms)

Version 2019.5.1

  • Add reverse parameter to the sorting functions.
  • Fix minor documentation formatting issues
  • Update installation instruction with conda install from conda-forge
  • Change the column names added to Experiment.feature_metadata after running Experiment.correlation or Experiment.diff_abundance

Version 2018.10.1

  • Add notebook tutorial for calour.training module for classification and regression.
  • Add notebook tutorial for metabolome data analysis
  • Add plot functions in calour.training module
  • Fix a bug in Expriment.aggregate_by_metadata when the number in the data table is overflow the int type.
  • Add CONTRIBUTING.md as guidelines
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