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---
title: "Cepo"
output: github_document
---
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<img src="man/figures/Cepo_logo.png" align="right" width="225" height="250"/>
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 [](https://codecov.io/gh/PYangLab/Cepo)
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Defining the identity of a cell is fundamental to understand the heterogeneity of cells to various environmental signals and perturbations. We present Cepo, a new method to explore cell identities from single-cell RNA-sequencing data using differential stability as a new metric to define cell identity genes. Cepo computes cell-type specific gene statistics pertaining to differential stable gene expression.
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## Installation
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You can install the development version of _Cepo_ that can be installed from GitHub
using the `remotes` package:
``` r
# install.packages("remotes")
remotes::install_github("PYangLab/Cepo")
```
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You can install the Bioconductor version of _Cepo_ from:
``` r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Cepo")
```
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To also build the vignettes use:
``` r
# install.packages("remotes")
remotes::install_github("PYangLab/Cepo", dependencies = TRUE,
build_vignettes = TRUE)
```
**NOTE:** Building the vignettes requires the installation of additional
packages.
## Documentation
The documentation for _Cepo_ is available from http://github.io/PYangLab/Cepo
To view the vignette and all the package documentation for the development
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version visit http://github.io/PYangLab/Cepo.
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## Citing _Cepo_
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If you use *Cepo* in your work please cite our preprint ["Kim H.J., Wang
K., Yang P. Cepo uncovers cell identity through
differential stability. bioRxiv DOI:](add%20biorxiv%20link).
To find all source code related to the anlayses of our preprint please refer to <http://github.io/PYangLab/CepoManuscript>.
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## Developers
The following individuals were involved in developing the Cepo package:
* [@HaniJieunKim](https://github.com/HaniJieunKim)
* [@kevinwang09](https://github.com/kevinwang09)
* [@PYangLab](https://github.com/PYangLab)
## Contact us
If you have any enquiries, especially about using Cepo to analyse your data, please contact [email protected]. We actively welcome any feedback and suggestions!
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