sccca (version 0.1.1)

Single-Cell Correlation Based Cell Type Annotation

Description

Performing cell type annotation based on cell markers from a unified database. The approach utilizes correlation-based approach combined with association analysis using Fisher-exact and phyper statistical tests (Upton, Graham JG. (1992) ).

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Version

Install

install.packages('sccca')

Monthly Downloads

192

Version

0.1.1

License

GPL (>= 3)

Maintainer

Mohamed Soudy

Last Published

March 13th, 2024

Functions in sccca (0.1.1)

correct_gene_symbols

Process the cell markers names

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

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

process_clus

Gets the associated cell types using correlation-based approach

calculate_cor_mat

Performs aggregation based on cell clusters and condition. Then, it calculates correlation matrix of genes

enrich_genes

Performs parallel function on two lists

calculate_normalized_ratio

Calculate cell scores based on number of genes

process_markers

Process the cell markers database and return the processed list

process_database

Process the database for the sctype approach

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.