All functions

EWCE 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_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

merge_ctd()

Merge multiple CellTypeDataset references

merge_sce()

Merge multiple SingleCellExperiment objects

merge_two_expfiles()

Merge two exp files

merged_ewce()

Multiple EWCE results from multiple studies

plot_ctd()

Plot CellTypeData metrics

prep.dendro()

prep.dendro

sct_normalize()

Normalize expression matrix

standardise_ctd()

Convert a CellTypeDataset into standardized format