├── BayesPrism ├── DESCRIPTION ├── NAMESPACE ├── R │ ├── JointPost_functions.R │ ├── Rcgminu.R │ ├── classes.R │ ├── embedding_learning.R │ ├── extract_result.R │ ├── generic.R │ ├── new_prism.R │ ├── optim_functions_MAP.R │ ├── optim_functions_MLE.R │ ├── plot_functions.R │ ├── process_input.R │ ├── run_gibbs.R │ ├── run_prism.R │ ├── run_prism_st.R │ └── update_reference.R ├── inst │ └── extdata │ │ ├── gencode.v22.broad.category.txt │ │ ├── genelist.hs.new.txt │ │ └── genelist.mm.new.txt └── man │ ├── cleanup.genes.Rd │ ├── collapse.Rd │ ├── get.exp.Rd │ ├── get.exp.stat.Rd │ ├── get.fraction.Rd │ ├── learn.embedding.Rd │ ├── learn.embedding.nmf.Rd │ ├── new.prism.Rd │ ├── plot.bulk.outlier.Rd │ ├── plot.bulk.vs.sc.Rd │ ├── plot.cor.phi.Rd │ ├── plot.scRNA.outlier.Rd │ ├── run.prism.Rd │ ├── select.gene.type.Rd │ ├── select.marker.Rd │ └── update.theta.Rd ├── README.md ├── img └── img1.png ├── tutorial.dat └── tutorial.gbm.rdata ├── tutorial_deconvolution.html ├── 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