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This package is for version 3.19 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see EWCE.

Expression Weighted Celltype Enrichment

Bioconductor version: Release (3.19)

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.

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

Maintainer: Alan Murphy <alanmurph94 at>

Citation (from within R, enter citation("EWCE")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Extended examples HTML R Script
Getting started HTML R Script
Reference Manual PDF


biocViews BiomedicalInformatics, DifferentialExpression, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, Microarray, OneChannel, Proteomics, RNASeq, SingleCell, Software, Transcription, Visualization, mRNAMicroarray
Version 1.12.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL-3
Depends R (>= 4.2), RNOmni (>= 1.0)
Imports stats, utils, methods, ewceData(>= 1.7.1), dplyr, ggplot2, reshape2, limma, stringr, HGNChelper, Matrix, parallel, SingleCellExperiment, SummarizedExperiment, DelayedArray, BiocParallel, orthogene(>= 0.99.8), data.table
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Suggests rworkflows, remotes, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), readxl, memoise, markdown, sctransform, DESeq2, MAST, DelayedMatrixStats, ggdendro, scales, patchwork
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Follow Installation instructions to use this package in your R session.

Source Package EWCE_1.12.0.tar.gz
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macOS Binary (x86_64) EWCE_1.12.0.tgz
macOS Binary (arm64) EWCE_1.12.0.tgz
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Source Repository (Developer Access) git clone
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