# BayesPrism: Bayesian cell type and gene expression deconvolution

## Documentation for package ‘BayesPrism’ version 2.0

- DESCRIPTION file.

## Help Pages

cleanup.genes | A function to filter genes by gene category and to exlcude lowly expressed genes.
collapse | Summing up reads across cells from each cell type/state
get.exp | Extract results from the BayesPrism object
get.exp.stat | The function to perform differential expression test for the selection of marker genes.
get.fraction | Extract results from the BayesPrism object
learn.embedding | Embedding learning
learn.embedding.nmf | Embedding learning
new.prism | Construct a prism object
plot.bulk.outlier | Visualize and determine outliers from the bulk mixture
plot.bulk.vs.sc | Make the bulk vs scRNA scatter plot by gene type (coding, lncRNA and psuedogenes)
plot.cor.phi | Plot correlation matrix for the reference profile phi
plot.scRNA.outlier | Visualize and determine outliers in scRNA-seq reference
run.prism | Main function to Run BayesPrism
select.gene.type | A function to select genes by gene type (e.g. "protein_coding", "pseudogene", "lincRNA" ).
select.marker | The function to perform differential expression test for the selection of marker genes.
update.theta | Update cell type fraction using output from the initial Gibbs sampling