Version 0.12.0

0.12.0 (19-12-24)

• add contrasts parameter to tools.marker_genes.run_deseq2
• tools.marker_genes.pairwise_rank_genes check minimum amount of groups

Changes to notebooks

• General: group_marker: set n_genes as top_n for get_rank_genes_tables
• ATAC 01 assembly: fix error when selecting the path_mtx (3rd) option (#326)
• General: prepare_for_cellxgene: set required mampok version to 3.0.5

Version 0.11.0

0.11.0 (08-11-24)

• fix pl.embedding.plot_pca_variance() does not select all PCs using thr 100% (#309)
• feature_per_group remove empty axis (#312)
• fix get_rank_genes_tables return less than n_genes for filtered ranking
• fix _search_dim_red_parameters "ValueError: 'left' is not a valid value for loc"
• fix gseapy, louvain install outside of the docker image (#310)
• implemented plotting.embedding.agg_feature_embedding
• cleanup installation/ dependencies
• CI: Revert to installing mampok from main
• implement bgcolor cell-selection
• update readme
• add a bar plot to predict_cell_cycle (#301)

Changes to notebooks

• add agg_feature_embedding to the group_marker notebook
• fix RNA:02 zebrafish gender suggestion (#311)
• revise 03_normalization_batch_correction notebook
• prepare_for_cellxgene: Add auth parameter
• use the bgcolor cell-selection in all notebooks

Version 0.7

0.7.0 (23-04-24)

• Added code examples for tools and utils (#140)
  • recluster
  • group_heatmap
  • plot_venn
  • in_range
• Fix notebooks in readthedocs documentation (#220)
• Removed custom_marker_annotation script
• Disintegrated FLD scoring and added PEAKQC to setup.py (#233)
• fixed PCA-var plot not fitting into anndata_overview (#232)

Changes to notebooks

• Overhaul RNA & ATAC notebooks structure (includes #207)
• Revise RNA notebook 4 recluster section (#201)