Man pages for NathanSkene/EWCE
Expression Weighted Celltype Enrichment

add_res_to_merging_listAdd to results to merging list
assign_coresAssign cores
bin_columns_into_quantiles'bin_columns_into_quantiles'
bin_specificity_into_quantilesbin_specificity_into_quantiles
bootstrap_enrichment_testBootstrap cell type enrichment test
bootstrap_plotBootstrap plot
calc_quantilesCalculate quantiles
calculate_meanexp_for_levelcalculate_meanexp_for_level
calculate_specificity_for_levelCalculate specificity for one CTD level
cell_list_distcell_list_dist
check_annotLevelscheck_annotLevels First, check the number of annotations...
check_args_for_bootstrap_plot_generationcheck_args_for_bootstrap_plot_generation
check_bootstrap_argscheck_bootstrap_args
check_controlled_argscheck_controlled_args
check_ewce_expression_data_argscheck_ewce_expression_data_args
check_ewce_genelist_inputscheck_ewce_genelist_inputs
check_full_resultscheck_full_results
check_generate_controlled_bootstrap_genesetgenerate_controlled_bootstrap_geneset
check_group_nameCheck group name
check_nasCheck NAs
check_numericCheck numeric
check_percent_hitsGet percentage of target cell type hits
check_sceCheck SingleCellExperiment
check_speciesCheck species
controlled_geneset_enrichmentCelltype controlled geneset enrichment
convert_new_ewce_to_oldconvert_new_ewce_to_old
convert_old_ewce_to_newconvert_old_ewce_to_new
create_background_multilistCreate background gene list for multiple species
create_list_network'create_list_network'
ctd_to_sceCellTypeDataset to SingleCellExperiment
delayedarray_normalizeEfficiently normalize a DelayedArray
drop_nonexpressed_cellsDrop cells with zero gene counts
drop_nonexpressed_genesDrop genes with zero counts
drop_uninformative_genesDrop uninformative genes
dt_to_dfConvert a 'data.table' to a 'data.frame'.
ewce_expression_dataBootstrap cell type enrichment test for transcriptome data
EWCE-packageEWCE: Expression Weighted Celltype Enrichment
ewce_plotPlot EWCE results
example_bootstrap_resultsExample bootstrap enrichment results
example_transcriptome_resultsExample bootstrap celltype enrichment test for transcriptome...
extract_matrixExtract a matrix from a CellTypeDataset
filter_ctd_genesFilter genes in a CellTypeDataset
filter_genes_without_1to1_homologfilter_genes_without_1to1_homolog
filter_nonorthologsFilter non-orthologs
filter_variance_quantilesFilter variance quantiles
fix_bad_hgnc_symbolsfix_bad_hgnc_symbols
fix_bad_mgi_symbolsfix_bad_mgi_symbols - Given an expression matrix, wherein the...
fix_celltype_namesFix celltype names
fix_celltype_names_full_resultsFix celltype name in full results
generate_bootstrap_plotsGenerate bootstrap plots
generate_bootstrap_plots_for_transcriptomeGenerate bootstrap plots
generate_celltype_dataGenerate CellTypeData (CTD) file
generate_controlled_bootstrap_genesetgenerate_controlled_bootstrap_geneset
get_celltype_tableget_celltype_table
get_ctd_levelsGet the names of CellTypeDataset levels
get_ctd_matrix_namesGet CTD matrix names
get_exp_data_for_bootstrapped_genesget_exp_data_for_bootstrapped_genes
get_graph_themeGet graph theme
get_sig_resultsExtract significant results
get_summed_proportionsGet summed proportions
is_32bitChecks whether OS is a 32-bit Windows
is_celltypedatasetCheck whether object is a CellTypeDataset
is_ctd_standardisedCheck whether a CellTypeDataset is standardised
is_delayed_arrayAssess whether an object is a DelayedArray.
is_matrixAssess whether an object is a Matrix
is_sparse_matrixAssess whether an object is a sparse matrix
list_speciesList all species
load_rdata'load_rdata'
max_ctd_depthGet max CTD depth
merge_ctdMerge multiple CellTypeDataset references
merged_ewceMultiple EWCE results from multiple studies
merge_sceMerge multiple 'SingleCellExperiment' objects
merge_sce_listMerge of list of SingleCellExperiment objects
merge_two_expfilesMerge two exp files
message_parallelPrint messages
messagerPrint messages
myScalesComma'myScalesComma'
plot_bootstrap_plotsBootstrap plot
plot_ctdPlot _CellTypeData_ metrics
plot_log_bootstrap_distributionsPlot log bootstrap distributions
plot_with_bootstrap_distributionsPlot with bootstrap distributions
prepare_genesize_control_networkPrepare genesize control network
prepare_ttPrepare differential gene expression table
prep_dendroPrepare dendrogram
prep.dendroprep.dendro
report_dgeReport DGE
report_resultsReport cell type enrichment results
run_deseq2Run DGE: 'DESeq2'
run_limmaRun DGE: 'limma'
run_mastRun DGE: 'MAST'
sce_lists_applysce_lists_apply
sce_merged_applysce_merged_apply
sct_normalizeNormalize expression matrix
standardise_ctdConvert a CellTypeDataset into standardized format
to_dataframeConvert object to data.frame
to_delayed_arrayConvert object to DelayedArray
to_sparse_matrixConvert object to sparse matrix
NathanSkene/EWCE documentation built on Aug. 6, 2022, 9:27 a.m.