Version 0.13.0

0.13.0 (08-08-25)

• predict_cell_cycle: implemented "gene_column" parameter
• restrict the maximum size of a figure (2^16 pixle)
• from_h5ad: expose concadata "label" parameter
• Add delete_obs and delete_var parameters to prepare_for_cellxgene() (#287)
• Add ability to use a peaks BED file to assemble var of ATAC-data (#346)
• set scanpy>=1.11 to fix run_rank_genes error (#331)
• GSEA: Revise gsea analysis: Bugfixes, save results into adata, rework plots (#345)
• Add column exists check to bioutils.pseudobulk_table (#356)
• Fix main title in receptor-ligand network plot (#358)
• load_h5ad(): warn if adata.raw is found. (#352)
• receptor-ligand: nan zscore to 0 (#302)
• adjust to altered scanpy.normalize_total behavior (#370)
• Add function to download tutorial data
• plot_pca_variance: add selected variance line; allow log-scale
• add global dpi setting
• implemented suppress_logging, get_version_report, plot_table, update_yml, generate_report
• Allow differential R-L plots to be asved as PDF
• receptor-ligand: adjust minimum line width in connectionPlot
• Added new notebook testdata and references. (partly #338)
• Improved flexibility in adata creation from mtx. (#365)
• lsi: fixed bug scaling the total variance explained to 100%

Changes to notebooks

• velocity: Changed scvelo.read() to scanpy.read() in the velocity notebook due to deprecation (#344)
• General: prepare_for_cellxgene: Set mampok version to 3.0.6
• General: prepare_for_cellxgene: Add metadata parameter for mamplan correlation
• General: prepare_for_cellxgene: Add delete column option for .obs and .var
• RNA 02 QC: fixed bug causing initial var thresholds to be ignored
• General: pseudotime_analysis: color dendrogram for clustering instead of segment
• add layer option to notebooks that utilize the matrix (#342)
• pptreport integration:
  • 01-RNA
  • 02-RNA
  • 03-RNA
  • 04-RNA
  • 0A1-RNA receptor-ligand
  • 0A2-RNA receptor-ligand differences
  • 0B-RNA velocity notebook
  • general group_markers
  • general pseudotime
  • general proportion
  • general GSEA
  • general annotation
  • 01-ATAC
  • 02-ATAC
  • 03-ATAC
  • 04-ATAC
• RNA: implemented report notebook
• General: annotation: add min_hits parameter
• RNA/ ATAC 03: allow to choose the number of computed PCs
• RNA/ ATAC 01: allow to choose batch name
• General: Move settings to config file
• velocity: Add missing save/embedding options
• atac_analysis: assembling: Changed to new testdata.
• ATAC: Implemented TOBIAS footprinting notebook
• General: Pseudotime: Remove threads parameter from dendrogram function