BayesPrism: Bayesian cell type and gene expression deconvolution

Documentation for package ‘BayesPrism’ version 2.0

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