Function reference • scFeatures

All functions

example_scrnaseq: Example of scRNA-seq data

get_num_cell_per_spot(): Estimate a relative number of cells per spot for spatial transcriptomics data

remove_mito_ribo(): Remove mitochondrial and ribosomal genes, and other highly correlated genes

run_CCI(): Generate cell cell communication score

run_L_function(): Generate L stats

run_Morans_I(): Generate Moran's I

run_association_study_report(): Create an association study report in HTML format

run_celltype_interaction(): Generate cell type interaction

run_gene_cor(): Generate overall aggregated gene correlation

run_gene_cor_celltype(): Generate cell type specific gene expression correlation

run_gene_mean(): Generate overall aggregated mean expression

run_gene_mean_celltype(): Generate cell type specific gene mean expression

run_gene_prop(): Generate overall aggregated gene proportion expression

run_gene_prop_celltype(): Generate cell type specific gene proportion expression

run_nn_correlation(): Generate nearest neighbour correlation

run_pathway_gsva(): Generate pathway score using gene set enrichement analysis

run_pathway_mean(): Generate pathway score using expression level

run_pathway_prop(): Generate pathway score using proportion of expression

run_proportion_logit(): Generate cell type proportions, with logit transformation

run_proportion_ratio(): Generate cell type proportion ratio

run_proportion_raw(): Generate cell type proportion raw

scFeatures(): Wrapper function to run all feature types in scFeatures

scfeatures_result: Example of scFeatures() output