Multiomics Analysis Identifies Chromosomal Instability-Associated Immune-Related Signatures in Hepatocellular Carcinoma by Integrating Weighted Gene Coexpression Network Analysis (WGCNA) and Machine Learning.

However, quantification of M2 macrophages varied across methods—xCell suggested a negative correlation, whereas Quantiseq showed a positive trend (Figure 5a ), highlighting the limitations of relying on a single algorithm to capture M2 macrophage dynamics.

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