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CHANGELOG
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CHANGELOG
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Version 0.2.0
* First stable version
Version 0.2.5
* Bug fixes
* Added more normalization methods
Version 0.3.0
* Bug fixes
* Optimized the normalization
* Unsupervised allows to center size factors by mean
* Unsupervised allows to computed adjusted log normalized counts
* Unsupervised allows to compute the number of clusters automatically
* Supervised allows to normalize the data
* Supervised allows to input train/classes with different spots
than in the train/test data and in different order
* st_data_plotter allows to highlight selected spots
* st_data_plotter only plots the spots where the gene is present
when a gene reg-exp is given
* st_data_plotter allows to normalize the data
* differential_analysis allows to normalize the data
* differential_analysis allows to input more than one dataset
Version 0.3.2
* The orientation of the cell tissue image is correct now
Version 0.3.3
* Fixed a bug in the visualization module
Version 0.4.0
* Removed deprecated scripts
* Adjusted some formats and parameters
Version 0.4.1
* Fixed a bug in the noise filtering function
Version 0.4.2
* Added compatibility with Python 3
Version 0.4.6
* Added merge_replicates.py script
* Added slice_regions_matrix.py script
* Optimized and improved differential_analysis.py
* Added compatibility with R 3.4 and rpy2 latest versions
Version 0.5.0
* Fixed bugs
* Added support for biocparalell
* Added extract_spots.py script
Version 0.5.1
* Small bug fixes
* Plots can be now generated in computers with not graphic card
* Improved the unsupervised.py script with a new clustering method
Version 0.5.2
* Added batch correction option to unsupervised.py
* Small improvements in unsupervised.py
* st_data_plotter3D.py can plot clusters
Version 0.5.3
* st_data_plotter.py can generate multiplots
* improvements in st_data_plotter.py
* unsupervised.py can generate multiplots
* remove color-space plots in unsupervised.py
Version 0.5.5
* Several improvements in supervised.py
* Added supervised_torch.py that does NN with PyTorch
* Improvements in the normalization and filtering
* Improvements in st_data_potter.py
Version 0.5.6
* Removed most of the R dependencies
* Added option to make a joint plot of a gene set in st_data_plotter
Version 0.6.0
* Removed R dependencies
* Improvements in data_plotter.py
* Improvements in unsupervised.py
* Removed deprecated scripts
* Added script to perform image/data alignment of consecutive sections
* Added script to plot genes and covariates onto a dimensionality reduced space (manifold)
* Added script to convert a Visium dataset to a ST dataset
Version 0.6.5
* Added script to combine (stitch) multiple datasets
* General improvements