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@Xiaojieqiu Xiaojieqiu released this 30 May 19:54
· 753 commits to master since this release
v1.3.0
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Dynamo Ver 1.3.0
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 PR 500). Check the tutorials here for more instructions.

Normalization has been refactored (PR 474 PR 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). 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). 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 PR 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). 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). 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), external data integration methods (PR 473) and pp.regress_out (PR 470 PR 483 PR 484).

Created more tests for preprocessing module (PR 485).

Replaced adata.obsm["X"] with adata.obsm["X_pca"] (PR 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.

DEBUG
Fixed the bug that save_show_or_return flags not working (PR 414).

Enabled the leiden algorithm to accept the resolution parameters (PR 441).

Fixed the wrong attribute name of anndata object in utils_dimensionReduction.py (PR 458)`

Fixed the dimensionality issue in moments.py (PR 461).

Fixed part of the bug that h5ad file cannot be saved correctly (PR 467).

Fixed the bug that pca_mean will be None under some circumstances (PR 482).

Removing warning message for nxviz (PR 489).

Corrected the norm log-likelihood function (PR 495).

Removed deprecated parameters in gseapy functions (PR 496).

Fixed the bugs that functions will raise error when no fixed points are found in vector field by sampling (PR 501).

Removed unwanted operations in dimension reduction (PR 502).

Tutorial Updates on Readthedocs
Documentation, Tutorials, and readthedocs update:

Update requirements for readthedocs (PR 466).

Update readme (PR 479).

Fixed documentation error caused by importing Literal (PR 486).

Fixed readthedocs error caused by the new version of urllib3 (PR 488).

Other Changes
Docstring and type hints update:

Updated docstring and type hints for tools module (PR 419).

Updated docstring and type hints for vector field module (PR 434).

Updated the docstring and type hints for simulation and predicting module (PR 457).

Update the docstring and type hints for hzplot (PR 456).

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