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Prepare a single-cell reference; i.e. CellTypeDataset (CTD). Alternatively, \nyou can use one of the pre-generated CTDs we provide via the package `ewceData`\n(which comes with *EWCE*).  \n2. Run cell type enrichment on a user-provided gene list.\n\n## Installation\n\n*EWCE* requires [`R\u003e=4.1`](https://www.r-project.org/) \nand `Bioconductor\u003e=3.14`. \nTo install *EWCE* on Bioconductor run:\n\n```{r, eval=FALSE}\nif (!require(\"BiocManager\")){install.packages(\"BiocManager\")}\n\nBiocManager::install(\"EWCE\") \n```\n\n## Documentation \n\n### [Website](https://`r owner`.github.io/`r pkg`/)  \n\n**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.  \n\n### [Getting started](https://`r owner`.github.io/`r pkg`/articles/`r pkg`)   \n\nIncludes:  \n\n- A minimal example to get started with running *EWCE*. \n- How to install and use the dedicated *EWCE* Docker container usage. [Docker](https://www.docker.com/) containers with the latest version of `EWCE` \nare regularly pushed to \n[Dockerhub](https://hub.docker.com/repository/docker/neurogenomicslab/ewce).  \n\n### [Extended examples](https://`r owner`.github.io/`r pkg`/articles/extended.html)\n\nAdditional tutorials of various *EWCE* features, including how to:  \n\n- Run cell-type enrichment tests \n- Create a CellTypeDataset\n- Merge two single-cell datasets \n- Run conditional cell-type enrichment tests\n- Apply to transcriptomic data\n \n## Updates\n\nMajor upgrades to *EWCE* were made in version 1.3.1.\nPlease see the [NEWS page](https://nathanskene.github.io/EWCE/news/index.html) for more details. \n\n## Troubleshooting\n\nIf you have any problems, please do submit an [Issue here on GitHub](https://github.com/nathanskene/EWCE/issues) with a reproducible example.\n\n## Citation\n\nIf you use ``r pkg``, please cite: \n\n\u003c!-- Modify this my editing the file: inst/CITATION  --\u003e\n\u003e `r citation(pkg)$textVersion`\n\nIf you use the cortex/hippocampus single-cell data associated \n*EWCE*/*ewceData* this package then please cite the following:\n\n\u003e [Zeisel, et al. Cell types in the mouse cortex and\nhippocampus revealed by single-cell RNA-seq. Science, 2015.\n](https://doi.org/10.1126/science.aaa1934)\n\n\u003chr\u003e \n\n## Contact\n \n### [Neurogenomics Lab](https://www.neurogenomics.co.uk/)\n\nUK Dementia Research Institute  \nDepartment of Brain Sciences  \nFaculty of Medicine  \nImperial College London   \n[GitHub](https://github.com/neurogenomics)  \n[DockerHub](https://hub.docker.com/orgs/neurogenomicslab)  \n\n## References\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnathanskene%2Fewce","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnathanskene%2Fewce","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnathanskene%2Fewce/lists"}