SPAC v0.9.1

What's Changed

• feat(qc-metrics): add common single cell quality control metrics by @abombin in #352
• feat(qc_summary_statistics): add summary statistics table for sc/spatial transcriptomics quality control metrics by @abombin in #353
• feat(visualize_ripley_template): add visualize_ripley_template and un… by @fangliu117 in #358
• feat(template_utils): add template_utils and unit tests by @fangliu117 in #356
• Refactor/ripley l template by @fangliu117 in #357
• Refactor: template-utils with review fixes by @fangliu117 in #359
• fix(ripley_template): address review comments - replace debug prints … by @fangliu117 in #360
• feat(setup_analysis_template): add setup_analysis_template function a… by @fangliu117 in #362
• Template load csv by @fangliu117 in #361
• feat(boxplot_template): add boxplot_template function and unit tests by @fangliu117 in #363
• feat(histogram_template): add histogram_template and unit tests by @fangliu117 in #364
• feat(spatial_plot_temp): add spatial_plot_template.py and unit tests by @fangliu117 in #365
• feat(arcsinh_normalization_template): add arcsinh_normalization_templ… by @fangliu117 in #366
• feat(zscore_normalization_template): add zscore_normalization_templat… by @fangliu117 in #367
• feat(summarize_dataframe_template): add summarize_dataframe_template … by @fangliu117 in #368
• feat(combine_annotations_template): add combine_annotations_template … by @fangliu117 in #369
• feat(manual_phenotyping_template): add manual_phenotyping_template fu… by @fangliu117 in #370
• feat(hierarchical_heatmap_template): add hierarchical_heatmap_templat… by @fangliu117 in #371
• feat(utag_clustering_template): add utag_clustering_template and unit… by @fangliu117 in #372
• feat(umap_transformation_template): add umap_transformation_template … by @fangliu117 in #373
• feat(phenograph_clustering_template): add phenograph_clustering_templ… by @fangliu117 in #374
• feat(umap_tsne_pca_template): add umap_tsne_pca_template function and… by @fangliu117 in #375
• feat(rename_labels_template): add rename_labels_template function and… by @fangliu117 in #376
• feat(relational_heatmap_template): add relational_heatmap_template fu… by @fangliu117 in #377
• feat(sankey_plot_template): add sankey_plot_template function and uni… by @fangliu117 in #378
• feat(neighborhood_profile_template): add neighborhood_profile_templat… by @fangliu117 in #379
• feat(analysis_to_csv_template): add analysis_to_csv_template function… by @fangliu117 in #380
• feat(summarize_annotation_statistics): add summarize_annotation_stati… by @fangliu117 in #381
• feat(interactive_spatial_plot_template): add interactive_spatial_plot… by @fangliu117 in #382
• feat(spatial_interaction_template): add spatial_interaction_template … by @fangliu117 in #383
• feat(nearest_neighbor_calculation_template): add nearest_neighbor_cal… by @fangliu117 in #384
• feat(visualize_nearest_neighbor_template): add visualize_nearest_neig… by @fangliu117 in #385
• feat(template_utils): add string_list_to_dictionary to template utils by @fangliu117 in #386
• feat(add_pin_color_rule_template): add add_pin_color_rule_template fn… by @fangliu117 in #387
• feat(append_annotation_template): add append_annotation_template func… by @fangliu117 in #388
• feat(binary_to_categorical_annotation_template): add binary_to_catego… by @fangliu117 in #389
• feat(calculate_centroid_template): add calculate_centroid_template fu… by @fangliu117 in #390
• feat(select_values_template): add select_values_template function and… by @fangliu117 in #391
• fix(select_values_template): fix pandas/numpy version compatibility i… by @fangliu117 in #392
• feat(downsample_cells_template): add downsample_cells_template functi… by @fangliu117 in #393
• feat(combine_dataframes_template): add combine_dataframes_template fu… by @fangliu117 in #394
• feat(subset_analysis_template): add subset_analysis_template function… by @fangliu117 in #395
• feat(quantile_scaling_template): refactor nidap code, add quantile_sc… by @fangliu117 in #396
• feat(normalize_batch_template): add normalize_batch_template function… by @fangliu117 in #397
• feat(tsne_analysis_template): add tsne_analysis_template function and… by @fangliu117 in #398
• feat(posit_it_python_template): add posit_it_python_template function… by @fangliu117 in #399
• feat: Add SPAC boxplot Galaxy tool for Docker deployment by @fangliu117 in #400
• feat: add spac arcsinh_norm interactive_spatial_plot galaxy tools by @fangliu117 in #401
• feat: add spac_setup_analysis galaxy tools by @fangliu117 in #402
• feat: add spac_zscore_normalization galaxy tools by @fangliu117 in #403
• refactor: streamline galaxy tools implementation by @fangliu117 in #405
• feat: add refactored galaxy tools by @fangliu117 in #407
• Benchmark script by @Ahmad8864 in #408
• fix(nearest_neighbor_template): Break the title in two lines by @georgezakinih in #409
• refactor all templates and unit tests by @fangliu117 in #415
• fix: Remove 6 deprecated templates (sync with tools_refactor) by @fangliu117 in #416
• merge dev to release_dev for updated spac templates by @fangliu117 in #417
• merge Release dev to main by @fangliu117 in #418

Full Changelog: v0.9.0-Public...v0.9.1