download License: GPL-3

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Authors: Alan Murphy, Brian Schilder, Nathan Skene

README updated: Nov-21-2023


The EWCE R package is designed to facilitate expression weighted cell type enrichment analysis as described in our Frontiers in Neuroscience paper1. EWCE can be applied to any gene list.

Using EWCE essentially involves two steps:

  1. Prepare a single-cell reference; i.e. CellTypeDataset (CTD). Alternatively, you can use one of the pre-generated CTDs we provide via the package ewceData (which comes with EWCE).
  2. Run cell type enrichment on a user-provided gene list.


EWCE requires R>=4.1 and Bioconductor>=3.14. To install EWCE on Bioconductor run:

if (!require("BiocManager")){install.packages("BiocManager")}




NOTE: This documentation is for the development version of EWCE. See Bioconductor for documentation on the current release version.

Getting started


  • A minimal example to get started with running EWCE.
  • How to install and use the dedicated EWCE Docker container usage. Docker containers with the latest version of EWCE are regularly pushed to Dockerhub.

Extended examples

Additional tutorials of various EWCE features, including how to:

  • Run cell-type enrichment tests
  • Create a CellTypeDataset
  • Merge two single-cell datasets
  • Run conditional cell-type enrichment tests
  • Apply to transcriptomic data


Major upgrades to EWCE were made in version 1.3.1. Please see the NEWS page for more details.


If you have any problems, please do submit an Issue here on GitHub with a reproducible example.


If you use EWCE, please cite:

Nathan G. Skene, Seth G. N. Grant (2016) Identification of Vulnerable Cell Types in Major Brain Disorders Using Single Cell Transcriptomes and Expression Weighted Cell Type Enrichment, Frontiers in Neuroscience; 10,

If you use the cortex/hippocampus single-cell data associated EWCE/ewceData this package then please cite the following:

Zeisel, et al. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science, 2015.


Neurogenomics Lab

UK Dementia Research Institute
Department of Brain Sciences
Faculty of Medicine
Imperial College London


Skene, N. & Grant, S. Identification of vulnerable cell types in major brain disorders using single cell transcriptomes and expression weighted cell type enrichment. Frontiers in Neuroscience (2016). doi:[10.3389/fnins.2016.00016](