title: "Cepo"
output: github_document
<img src="man/figures/Cepo_logo.png" align="right" width="225" height="250"/>

![R-CMD-check](https://github.com/PYangLab/Cepo/workflows/R-CMD-check/badge.svg) [![Codecov test coverage](https://codecov.io/gh/PYangLab/Cepo/branch/main/graph/badge.svg?token=sJROwPzwey)](https://codecov.io/gh/PYangLab/Cepo)

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. 

## Installation

You can install the development version of _Cepo_ that can be installed from GitHub
using the `remotes` package:

``` r
# install.packages("remotes")

You can install the Bioconductor version of _Cepo_ from:

``` r
if (!requireNamespace("BiocManager", quietly = TRUE))

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

## 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
version visit http://github.io/PYangLab/Cepo.

## Citing _Cepo_

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>.

## 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 hani.kim@sydney.edu.au. We actively welcome any feedback and suggestions!