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CDState is an unsupervised deconvolution method for tumor bulk RNA‑sequencing data that identifies transcriptional cell states of malignant cells and estimates their proportions across samples. without the need for reference data.
CDState takes as input a normalized bulk RNA‑seq expression matrix (X) and tumor purity estimates, and returns (1) gene expression profiles of inferred cell states (W), (2) their sample-wise proportions (H), and (3) an assignment of each state to the malignant (MAL) or tumor microenvironment (TME) compartment.