omicverse 1.7.0

v1.7.0

on Python PyPI

Added cpu-gpu-mixed to accelerate the analysis of scrna-seq using GPU.
Changed the logo presentation of Omicverse to ov.plot_set

Bulk Module

• Added limma, edgeR in different expression gene analysis. (#238)
• Fixed the version error of DEseq2 analysis.

Single Module

• Added lazy function to calculate all function of scrna-seq (#291)
• Added generate_scRNA_report and generate_reference_table to generate the report and reference (#291) (#292)
• Fixed geneset_prepare not being able to read gmt not split by \t\t (#235) (#238)
• Added geneset_aucell_tmp,pathway_aucell_tmp,pathway_aucell_enrichment_tmp to test the chunk_size (#238)
• Added data enhancement of Fate
• Added plot_atlas_view_ov in VIA
• Fixed an error when the matrix is too large in recover_counts.
• Added forceatlas2 to calculate the X_force_directed.
• Added milo and scCODA to analysis different celltype abundance.
• Added memento to analysis different gene expression.

Space Module

• Added GASTON to learn a topographic map of a tissue slice from spatially resolved transcriptomics (SRT) data (#238)
• Added super kwargs in plot_tensor_single of STT.
• Updated COMMOT using GPU-accerlate

Plot Module

• Added dotplot_doublegroup to visual the genes in doublegroup.
• Added transpose argument of cpdb_interacting_heatmap to transpose the figure.
• Added calculate_gene_density to plot the gene's density.