---
title: "`EWCE`: `E`xpression `W`eighted `C`elltype `E`nrichment"
author: "`r rworkflows::use_badges(add_bioc_release = TRUE, add_bioc_download_month = TRUE, add_bioc_download_rank = TRUE, add_bioc_download_total = TRUE)`"
date: "<h4>README updated: <i>`r format( Sys.Date(), '%b-%d-%Y')`</i></h4>"
bibliography: inst/cit/EWCE.bib
csl: inst/cit/nature.csl
output:
github_document
---
<!-- To modify Package/Title/Description/Authors fields, edit the DESCRIPTION file -->
```{r setup, echo=FALSE, include=FALSE}
pkg <- read.dcf("DESCRIPTION", fields = "Package")[1]
title <- read.dcf("DESCRIPTION", fields = "Title")[1]
description <- read.dcf("DESCRIPTION", fields = "Description")[1]
URL <- read.dcf('DESCRIPTION', fields = 'URL')[1]
owner <- strsplit(URL,"/")[[1]][4]
repo <- strsplit(URL,"/")[[1]][5]
```
## Introduction
The *EWCE* R package is designed to facilitate expression weighted cell type
enrichment analysis as described in our *Frontiers in Neuroscience*
paper [@skene_2016]. *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`](https://www.r-project.org/)
and `Bioconductor>=3.14`.
To install *EWCE* on Bioconductor run:
```{r, eval=FALSE}
if (!require("BiocManager")){install.packages("BiocManager")}
BiocManager::install("EWCE")
```
## Documentation
### [Website](https://`r owner`.github.io/`r pkg`/)
**NOTE**: This documentation is for the development version of ``r pkg``. See [Bioconductor](https://bioconductor.org/packages/release/bioc/html/EWCE.html) for documentation on the current release version.
### [Getting started](https://`r owner`.github.io/`r pkg`/articles/`r pkg`)
Includes:
- A minimal example to get started with running *EWCE*.
- How to install and use the dedicated *EWCE* Docker container usage. [Docker](https://www.docker.com/) containers with the latest version of `EWCE`
are regularly pushed to
[Dockerhub](https://hub.docker.com/repository/docker/neurogenomicslab/ewce).
### [Extended examples](https://`r owner`.github.io/`r pkg`/articles/extended.html)
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](https://nathanskene.github.io/EWCE/news/index.html) for more details.
## Troubleshooting
If you have any problems, please do submit an [Issue here on GitHub](https://github.com/nathanskene/EWCE/issues) with a reproducible example.
## Citation
If you use ``r pkg``, please cite:
<!-- Modify this my editing the file: inst/CITATION -->
> `r citation(pkg)$textVersion`
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.
](https://doi.org/10.1126/science.aaa1934)
<hr>
## Contact
### [Neurogenomics Lab](https://www.neurogenomics.co.uk/)
UK Dementia Research Institute
Department of Brain Sciences
Faculty of Medicine
Imperial College London
[GitHub](https://github.com/neurogenomics)
[DockerHub](https://hub.docker.com/orgs/neurogenomicslab)
## References
