Scaden Changelog
Version 1.1.2
- Changed datatype for data simulation back to
float32
Version 1.1.1
- Fixed bugs in scaden model definition [#88]
- removed installation instructions for bioconda as not functional at the moment [#86]
- Fixed bug in
scaden example
[#85]
Version 1.1.0
- Reduced memory usage of
scaden simulate
significantly by performing simulation for one dataset at a time. - Using
.h5ad
format to store simulated data - Allow reading data in
.h5ad
format for improved performance (courtesy of @eboileau) - Improved logging and using rich progress bar for training
- Gene subsetting is now done only when merging datasets, which will allow to generate different combinations of simulated datasets
- Added
scaden merge
command which allows merging of previously created datasets
Version 1.0.2
- General improvement of logging using the 'rich' library for colorized output
- Added verification check for '--train_datasets' parameter to notify user of unavailable datasets
Version 1.0.1
- Made identification of datasets more robust to fix issue #66
Version 1.0.0
- Rebuild Scaden model and training to use TF2 Keras API instead of the old compatibility functions
- added
scaden example
command which allows to generate example data for test-running scaden and to inpstec the expected file format - added more tests and checks input reading function in
scaden simulate
- fixed bug in reading input data
Version 0.9.6
- fixed Dockerfile (switched to pip installation)
- added better error messages to
simulate
command - cleaned up dependencies
v0.9.5
- added
--seed
parameter to allow reproducible Scaden runs - added
scaden simulate
command to perform bulk simulation and training file creation - changed CLI calling
v0.9.4
- fixed dependencies (added python>=3.6 requirement)
v0.9.3
- upgrade to tf2
- cleaned up dependencies
v0.9.2
- small code refactoring
- RAM usage improvement
v0.9.1
- added automatic removal of duplicate genes
- changed name of prediction file
v0.9.0
Initial release of the Scaden deconvolution package.
Commands:
scaden process
: Process a training dataset for trainingscaden train
: Train a Scaden modelscaden predict
: Predict cell type compositions of a given sample