`EWCE`: `E`xpression `W`eighted `C`elltype `E`nrichment ================ <img src='https://github.com/NathanSkene/EWCE/raw/master/inst/hex/hex.png' title='Hex sticker for EWCE' height='300'><br> [](https://www.bioconductor.org/packages/EWCE) [](https://bioconductor.org/packages/stats/bioc/EWCE) [](https://bioconductor.org/packages/stats/bioc/EWCE) [](https://bioconductor.org/packages/stats/bioc/EWCE) [](https://cran.r-project.org/web/licenses/GPL-3) <br> [](https://github.com/NathanSkene/EWCE) [](https://github.com/NathanSkene/EWCE) [](https://github.com/NathanSkene/EWCE/commits/master) <br> [](https://github.com/NathanSkene/EWCE/actions) [](https://app.codecov.io/gh/NathanSkene/EWCE) <br> <a href='https://app.codecov.io/gh/NathanSkene/EWCE/tree/master' target='_blank'><img src='https://codecov.io/gh/NathanSkene/EWCE/branch/master/graphs/icicle.svg' title='Codecov icicle graph' width='200' height='50' style='vertical-align: top;'></a> <h4> Authors: <i>Alan Murphy, Brian Schilder, Nathan Skene</i> </h4> <h4> README updated: <i>Jul-09-2024</i> </h4> <!-- To modify Package/Title/Description/Authors fields, edit the DESCRIPTION file --> ## 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`](https://www.r-project.org/) and `Bioconductor>=3.14`. To install *EWCE* on Bioconductor run: ``` r if (!require("BiocManager")){install.packages("BiocManager")} BiocManager::install("EWCE") ``` ## Documentation ### [Website](https://NathanSkene.github.io/EWCE/) **NOTE**: This documentation is for the development version of `EWCE`. See [Bioconductor](https://bioconductor.org/packages/release/bioc/html/EWCE.html) for documentation on the current release version. ### [Getting started](https://NathanSkene.github.io/EWCE/articles/EWCE) 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://NathanSkene.github.io/EWCE/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 `EWCE`, please cite: <!-- Modify this my editing the file: inst/CITATION --> > 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.](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 <div id="refs" class="references csl-bib-body" line-spacing="2"> <div id="ref-skene_2016" class="csl-entry"> <span class="csl-left-margin">1. </span><span class="csl-right-inline">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](https://doi.org/10.3389/fnins.2016.00016)</span> </div> </div>