bulk-rna-seq-deconvolution-with-bulk2single

核心说明

• Use this skill when user wants to reconstruct single-cell profiles ，面向 bulk RNA-seq together ，支持 matched reference scRNA-seq atlas. It follows t_bulk2single.ipynb，which demonstrates how to harmonise PDAC bulk replicates，train beta-VAE generator，、 benchmark output cells against dentate gyrus scRNA-seq。
• Import omicverse as ov，scanpy as sc，scvelo as scv，anndata，、 matplotlib.pyplot as plt，then call ov.plot_set() to match omicverse styling。
• Read bulk counts table ，支持 ov.read(...)/ov.utils.read(...) 、 harmonise gene identifiers ，通过 ov.bulk.Matrix_ID_mapping(<df>，'genesets/pair_GRCm39.tsv')。
• Load reference scRNA-seq AnnData (e.g.，scv.数据集s.dentategyrus()) 、 confirm cluster labels (stored in adata.obs['clusters'])。
• Instantiate ov.bulk2single.Bulk2Single(bulk_data=bulk_df，single_data=adata，celltype_key='clusters'，bulk_group=['dg_d_1'，'dg_d_2'，'dg_d_3']，top_marker_num=200，ratio_num=1，gpu=0)。