Single-Cell Correlation Based Cell Type Annotation

Documentation for package ‘sccca’ version 0.1.1

calculate_cor_mat	Performs aggregation based on cell clusters and condition. Then, it calculates correlation matrix of genes
calculate_normalized_ratio	Calculate cell scores based on number of genes
correct_gene_symbols	Process the cell markers names
enrich_genes	Performs parallel function on two lists
filter_correlation	Filter the genes based on specific correlation threshold
filter_list	Process the cell markers that overlap between the cell markers and scRNA matrix
fisher_test	Performs fisher exact test to get the significant overlap between genes for cell type assignment
match_characters	Process the cell markers that pass specific threshold in the gene correlation matrix
phyper_test	Performs phyper test to get the significant overlap between genes for cell type assignment
process_clus	Gets the associated cell types using correlation-based approach
process_database	Process the database for the sctype approach
process_markers	Process the cell markers database and return the processed list
sccca	Run the pipeline for the cell type assignment
sctype	Run the sctype approach as it's implemented by Ianevski, A., Giri, A.K. and Aittokallio, T.