mengxu98 / ewce

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

EWCE: Expression Weighted Celltype Enrichment

Authors: Alan Murphy, Brian Schilder, Nathan Skene

README updated: Apr-03-2023

Introduction

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.

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 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

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:

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

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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