Dynamo Ver 1.3.0[](https://dynamo-release.readthedocs.io/en/latest/Release_notes.html#dynamo-ver-1-3-0)
Feature Changes[](https://dynamo-release.readthedocs.io/en/latest/Release_notes.html#feature-changes)
The preprocessing module has been refactored:
Class Preprocessor is recommended for most preprocessing methods and recipes. pp.recipe_monocle, pp.recipe_velocyto has been deprecated ([PR 497](https://github.com/aristoteleo/dynamo-release/pull/497) [PR 500](https://github.com/aristoteleo/dynamo-release/pull/500)). Check the tutorials [here](https://dynamo-release.readthedocs.io/en/latest/Preprocessor_tutorial.html) for more instructions.
Normalization has been refactored ([PR 474](https://github.com/aristoteleo/dynamo-release/pull/474) [PR 475](https://github.com/aristoteleo/dynamo-release/pull/475)): pp.normalize_cell_expr_by_size_factors has been deprecated, and new APIs are:
pp.normalize_cell_expr_by_size_factors -> pp.calc_sz_factor, pp.normalize.
Gene selection has been refactored ([PR 474](https://github.com/aristoteleo/dynamo-release/pull/474)). Now support genes selected by fano factors. APIs are pp.select_genes_monocle and pp.select_genes_by_seurat_recipe.
PCA has been refactored ([PR 469](https://github.com/aristoteleo/dynamo-release/pull/469)). dyn.pp.pca_monocle has been deprecated. The new API is:
pp.pca_monocle -> pp.pca.
sctransform and pearson residuals recipe has been refactored ([PR 510](https://github.com/aristoteleo/dynamo-release/pull/510) [PR 512](https://github.com/aristoteleo/dynamo-release/pull/512)). Now those advanced methods will only be performed on X layer. Other layers will get normalized by size factors.
Calculation of ntr rate and pp.cell_cycle_scores has been added to the Preprocessor ([PR 513](https://github.com/aristoteleo/dynamo-release/pull/513)). To enable cell cycle scores, set parameter cell_cycle_score_enable to True when initializing the pp.Preprocessor.
Now the size factors normalization will normalize all layers with its own size factors by default ([PR 521](https://github.com/aristoteleo/dynamo-release/pull/521)). To normalize the labeled data with total size factors, we need to set the total_szfactor to total_Size_Factor explicitly.
Multiple new features added, includes genes selection by fano factors ([PR 474](https://github.com/aristoteleo/dynamo-release/pull/474)), external data integration methods ([PR 473](https://github.com/aristoteleo/dynamo-release/pull/473)) and pp.regress_out ([PR 470](https://github.com/aristoteleo/dynamo-release/pull/470) [PR 483](https://github.com/aristoteleo/dynamo-release/pull/483) [PR 484](https://github.com/aristoteleo/dynamo-release/pull/484)).
Created more tests for preprocessing module ([PR 485](https://github.com/aristoteleo/dynamo-release/pull/485)).
Replaced adata.obsm["X"] with adata.obsm["X_pca"] ([PR 514](https://github.com/aristoteleo/dynamo-release/pull/514)).
Removed some console output. They can still be displayed with DEBUG logging mode.
Other deprecated APIs include: pp.calc_sz_factor_legacy, pp.filter_cells_legacy, pp.filter_genes_by_outliers_legacy, pp.select_genes_monocle_legacy, pp.select_genes_by_dispersion_general, pp.cook_dist, pp.normalize_cell_expr_by_size_factors. More information can be found on our [preprocessing tutorials](https://dynamo-release.readthedocs.io/en/latest/Preprocessor_tutorial.html).
DEBUG[](https://dynamo-release.readthedocs.io/en/latest/Release_notes.html#debug)
Fixed the bug that save_show_or_return flags not working ([PR 414](https://github.com/aristoteleo/dynamo-release/pull/414)).
Enabled the leiden algorithm to accept the resolution parameters ([PR 441](https://github.com/aristoteleo/dynamo-release/pull/441)).
Fixed the wrong attribute name of anndata object in utils_dimensionReduction.py ([PR 458](https://github.com/aristoteleo/dynamo-release/pull/458))`
Fixed the dimensionality issue in moments.py ([PR 461](https://github.com/aristoteleo/dynamo-release/pull/461)).
Fixed part of the bug that h5ad file cannot be saved correctly ([PR 467](https://github.com/aristoteleo/dynamo-release/pull/467)).
Fixed the bug that pca_mean will be None under some circumstances ([PR 482](https://github.com/aristoteleo/dynamo-release/pull/482)).
Removing warning message for nxviz ([PR 489](https://github.com/aristoteleo/dynamo-release/pull/489)).
Corrected the norm log-likelihood function ([PR 495](https://github.com/aristoteleo/dynamo-release/pull/495)).
Removed deprecated parameters in gseapy functions ([PR 496](https://github.com/aristoteleo/dynamo-release/pull/496)).
Fixed the bugs that functions will raise error when no fixed points are found in vector field by sampling ([PR 501](https://github.com/aristoteleo/dynamo-release/pull/501)).
Removed unwanted operations in dimension reduction ([PR 502](https://github.com/aristoteleo/dynamo-release/pull/502)).
Tutorial Updates on Readthedocs[](https://dynamo-release.readthedocs.io/en/latest/Release_notes.html#tutorial-updates-on-readthedocs)
Documentation, Tutorials, and readthedocs update:
Update requirements for readthedocs ([PR 466](https://github.com/aristoteleo/dynamo-release/pull/466)).
Update readme ([PR 479](https://github.com/aristoteleo/dynamo-release/pull/479)).
Fixed documentation error caused by importing Literal ([PR 486](https://github.com/aristoteleo/dynamo-release/pull/486)).
Fixed readthedocs error caused by the new version of urllib3 ([PR 488](https://github.com/aristoteleo/dynamo-release/pull/488)).
Other Changes[](https://dynamo-release.readthedocs.io/en/latest/Release_notes.html#other-changes)
Docstring and type hints update:
Updated docstring and type hints for tools module ([PR 419](https://github.com/aristoteleo/dynamo-release/pull/419)).
Updated docstring and type hints for vector field module ([PR 434](https://github.com/aristoteleo/dynamo-release/pull/434)).
Updated the docstring and type hints for simulation and predicting module ([PR 457](https://github.com/aristoteleo/dynamo-release/pull/457)).
Update the docstring and type hints for hzplot ([PR 456](https://github.com/aristoteleo/dynamo-release/pull/456)).