Cepo ================ <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") remotes::install_github("PYangLab/Cepo") ``` 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.com/PYangLab/Cepo> To view the vignette and all the package documentation for the development version visit <http://github.com/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:](https://www.biorxiv.org/content/10.1101/2021.01.10.426138v1). To find all source code related to the anlayses of our preprint please refer to <http://github.com/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\!