https://github.com/biocore/calour - version 2020.8.6

Incompatible changes: * Change randomseed to work with numpy.random.defaultrng. This may cause different random numbers compared to the old versions using numpy.random.seed(). * Change parameter names in some functions * Rename filterabundance() to filtersum(abundance) * Other backwards incompatible function API changes and code refactoring.

New features: * Add RatioExperiment for working with ratios between two groups of features * Add randomseed option to tranforming.permutedata() * Add badcolor 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 featuremetadata field ("qval") for results of diffabundance() / correlation() * improved GUI for qt5 heatmap database enrichment results. * Add `readqiime2()function to enable reading of qiime2 feature tables artifacts with the associated representative sequences and taxonomy artifacts (without the need to install qiime2) * AddExperiment.validate(). * Change default color scale in heatmap plot to linear scale forExperimentand log scale forAmpliconExperimentandMS1Experiment`. * 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

- Python
Published by amnona almost 4 years ago

https://github.com/biocore/calour - Release 2019.5.1

This release has minor doc and functionality improvement.

- Python
Published by RNAer about 7 years ago

https://github.com/biocore/calour - release 2018.10.1

This release fixed a few minor bugs and improved documentation. The details is in change history

- Python
Published by RNAer over 7 years ago

https://github.com/biocore/calour - beta release

This is a beta release for calour. It provides interactive, exploratory analysis for 2 dimensional tables with metadata (like 16S microbiome table, gene abundance table, or metabolome table). The documentation is here.

- Python
Published by RNAer over 8 years ago