Additional file 1 of GTM-decon: guided-topic modeling of single-cell transcriptomes enables sub-cell-type and disease-subtype deconvolution of bulk transcriptomes

Abstract

Additional file 1. Supplementary Section S1 (Evaluation on gene selection strategies); S2 (Evaluation on raw count and transformation strategies); S3 (Experimenting hyperparameters $$\alpha_{\mathrm m,\mathrm k}$$ α m , k for cell-type mixture prior); S4 (Experimenting hyperparameter $$\beta$$ β for CTS topics); S5 (Experimenting number of topics per cell type); S6 (Benchmark time and memory usage); S7 (Effect of sparsification on phenotype classification); S8 (Phenotype-CTS topic modeling of single-cell breast cancer transcriptomes for TCGA-BRCA bulk deconvolution); S9 (Effect of cell size on inference of cell-type deconvolution); Table S1-S3; Figure S1-S31