Package: EWCE 1.13.0

Alan Murphy

EWCE: Expression Weighted Celltype Enrichment

Used to determine which cell types are enriched within gene lists. The package provides tools for testing enrichments within simple gene lists (such as human disease associated genes) and those resulting from differential expression studies. The package does not depend upon any particular Single Cell Transcriptome dataset and user defined datasets can be loaded in and used in the analyses.

Authors:Alan Murphy [cre], Brian Schilder [aut], Nathan Skene [aut]

EWCE_1.13.0.tar.gz
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EWCE_1.13.0.tgz(r-4.4-any)EWCE_1.13.0.tgz(r-4.3-any)
EWCE_1.13.0.tar.gz(r-4.5-noble)EWCE_1.13.0.tar.gz(r-4.4-noble)
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EWCE.pdf |EWCE.html✨
EWCE/json (API)
NEWS

# Install 'EWCE' in R:
install.packages('EWCE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/nathanskene/ewce/issues

On BioConductor:EWCE-1.13.0(bioc 3.20)EWCE-1.12.0(bioc 3.19)

bioconductor-package

32 exports 1.45 score 190 dependencies 13 mentions

Last updated 2 months agofrom:ce52346262

Exports:add_res_to_merging_listbin_columns_into_quantilesbin_specificity_into_quantilesbootstrap_enrichment_testcheck_ewce_genelist_inputscheck_percent_hitscontrolled_geneset_enrichmentctd_to_scedrop_uninformative_genesewce_expression_dataewce_plotexample_bootstrap_resultsexample_transcriptome_resultsfilter_ctd_genesfilter_genes_without_1to1_homologfilter_nonorthologsfix_bad_hgnc_symbolsfix_bad_mgi_symbolsfix_celltype_namesgenerate_bootstrap_plotsgenerate_bootstrap_plots_for_transcriptomegenerate_celltype_dataget_celltype_tablelist_speciesload_rdatamerge_ctdmerge_scemerge_two_expfilesmerged_ewceplot_ctdsct_normalizestandardise_ctd

Dependencies:abindAnnotationDbiAnnotationHubapeaplotaskpassbabelgenebackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobbootbriobroombslibcachemcallrcarcarDataclicliprcodetoolscolorspacecorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydescdiffobjdigestdplyrevaluateewceDataExperimentHubfansifarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggfunggplot2ggplotifyggpubrggrepelggsciggsignifggtreegluegprofiler2gridExtragridGraphicsgrrgtableHGNChelperhighrhmshomologenehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmimeminqamunsellnlmenloptrnnetnumDerivopensslorthogenepatchworkpbkrtestpillarpkgbuildpkgconfigpkgloadplogrplotlyplyrpngpolynompraiseprettyunitsprocessxprogresspromisespspurrrquantregR.cacheR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreadrrematch2repmisreshape2rlangrmarkdownRNOmnirprojrootRSQLiterstatixS4ArraysS4VectorssassscalesSingleCellExperimentsnowSparseArraySparseMsplitstackshapestatmodstringistringrSummarizedExperimentsurvivalsystestthattibbletidyrtidyselecttidytreetinytextreeiotzdbUCSC.utilsutf8vctrsviridisLitevroomwaldowithrxfunXVectoryamlyulab.utilszlibbioc

Readme and manuals

Help Manual

Help pageTopics
EWCE: Expression Weighted Celltype EnrichmentEWCE-package EWCE
Add to results to merging listadd_res_to_merging_list
'bin_columns_into_quantiles'bin_columns_into_quantiles
bin_specificity_into_quantilesbin_specificity_into_quantiles
Bootstrap cell type enrichment testbootstrap_enrichment_test
check_ewce_genelist_inputscheck_ewce_genelist_inputs
Get percentage of target cell type hitscheck_percent_hits
Celltype controlled geneset enrichmentcontrolled_geneset_enrichment
CellTypeDataset to SingleCellExperimentctd_to_sce
Drop uninformative genesdrop_uninformative_genes
Bootstrap cell type enrichment test for transcriptome dataewce_expression_data
Plot EWCE resultsewce_plot
Example bootstrap enrichment resultsexample_bootstrap_results
Example bootstrap celltype enrichment test for transcriptome dataexample_transcriptome_results
Filter genes in a CellTypeDatasetfilter_ctd_genes
filter_genes_without_1to1_homologfilter_genes_without_1to1_homolog
Filter non-orthologsfilter_nonorthologs
fix_bad_hgnc_symbolsfix_bad_hgnc_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_bad_mgi_symbols
Fix celltype namesfix_celltype_names
Generate bootstrap plotsgenerate_bootstrap_plots
Generate bootstrap plotsgenerate_bootstrap_plots_for_transcriptome
Generate CellTypeData (CTD) filegenerate_celltype_data
get_celltype_tableget_celltype_table
Assess whether an object is a DelayedArray.is_delayed_array
Assess whether an object is a Matrixis_matrix
Assess whether an object is a sparse matrixis_sparse_matrix
List all specieslist_species
'load_rdata'load_rdata
Merge multiple CellTypeDataset referencesmerge_ctd
Merge multiple 'SingleCellExperiment' objectsmerge_sce
Merge two exp filesmerge_two_expfiles
Multiple EWCE results from multiple studiesmerged_ewce
Plot _CellTypeData_ metricsplot_ctd
prep.dendroprep.dendro
Normalize expression matrixsct_normalize
Convert a CellTypeDataset into standardized formatstandardise_ctd