README.Rmd
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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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 ![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)
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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!