# Expression Weighted Celltype Enrichment

## Documentation for package ‘EWCE’ version 1.20.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

EWCE-package | EWCE: Expression Weighted Celltype Enrichment
add_res_to_merging_list | Add to results to merging list
bin_columns_into_quantiles | 'bin_columns_into_quantiles'
bin_specificity_into_quantiles | bin_specificity_into_quantiles
bootstrap_enrichment_test | Bootstrap cell type enrichment test
check_ewce_genelist_inputs | check_ewce_genelist_inputs
check_percent_hits | Get percentage of target cell type hits
controlled_geneset_enrichment | Celltype controlled geneset enrichment
ctd_to_sce | CellTypeDataset to SingleCellExperiment
drop_uninformative_genes | Drop uninformative genes
EWCE | EWCE: Expression Weighted Celltype Enrichment
ewce_expression_data | Bootstrap cell type enrichment test for transcriptome data
ewce_plot | Plot EWCE results
example_bootstrap_results | Example bootstrap enrichment results
example_transcriptome_results | Example bootstrap celltype enrichment test for transcriptome data
filter_ctd_genes | Filter genes in a CellTypeDataset
filter_genes_without_1to1_homolog | filter_genes_without_1to1_homolog
filter_nonorthologs | Filter non-orthologs
fix_bad_hgnc_symbols | fix_bad_hgnc_symbols
fix_bad_mgi_symbols | fix_bad_mgi_symbols - Given an expression matrix, wherein the rows are supposed to be MGI symbols, find those symbols which are not official MGI symbols, then check in the MGI synonm database for whether they match to a proper MGI symbol. Where a symbol is found to be an aliases for a gene that is already in the dataset, the combined reads are summed together.
fix_celltype_names | Fix celltype names
generate_bootstrap_plots | Generate bootstrap plots
generate_bootstrap_plots_for_transcriptome | Generate bootstrap plots
generate_celltype_data | Generate CellTypeData (CTD) file
get_celltype_table | get_celltype_table
is_delayed_array | Assess whether an object is a DelayedArray.
is_matrix | Assess whether an object is a Matrix
is_sparse_matrix | Assess whether an object is a sparse matrix
list_species | List all species
load_rdata | 'load_rdata'
merged_ewce | Multiple EWCE results from multiple studies
merge_ctd | Merge multiple CellTypeDataset references
merge_sce | Merge multiple 'SingleCellExperiment' objects
merge_two_expfiles | Merge two exp files
plot_ctd | Plot _CellTypeData_ metrics
prep.dendro | prep.dendro
sct_normalize | Normalize expression matrix
standardise_ctd | Convert a CellTypeDataset into standardized format