EWCE: Expression Weighted Celltype Enrichment
Authors: Alan Murphy, Brian Schilder, Nathan Skene
README updated: Feb-09-2022
Introduction
The EWCE R package is designed to facilitate expression weighted cell type enrichment analysis as described in our Frontiers in Neuroscience paper.1 EWCE can be applied to any gene list.
Using EWCE essentially involves two steps:
- 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). - Run cell type enrichment on a user-provided gene list.
Installation
EWCE requires R>=4.1 and
Bioconductor>=3.14. To install EWCE on Bioconductor run:
if (!require("BiocManager")){install.packages("BiocManager")}
BiocManager::install("EWCE") Documentation
Website
NOTE: This documentation is for the development version of EWCE.
See
Bioconductor
for documentation on the current release version.
Getting started
Includes:
- 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
EWCEare 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
Updates
Major upgrades to EWCE were made in version 1.3.1. Please see the NEWS page for more details.
Troubleshooting
If you have any problems, please do submit an Issue here on GitHub with a reproducible example.
Citation
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, https://doi.org/10.3389/fnins.2016.00016
If you use the cortex/hippocampus single-cell data associated EWCE/ewceData this package then please cite the following:
Contact
Neurogenomics Lab
UK Dementia Research Institute
Department of Brain Sciences
Faculty of Medicine
Imperial College London
GitHub
DockerHub
References
1. 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