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.
You can install the Bioconductor version of Cepo from:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Cepo")You can install the development version of Cepo from GitHub using the
remotes package:
# install.packages("remotes")
remotes::install_github("PYangLab/Cepo")To also build the vignettes use:
# install.packages("remotes")
remotes::install_github("PYangLab/Cepo", dependencies = TRUE,
build_vignettes = TRUE)NOTE: Building the vignettes requires the installation of additional packages.
The documentation for Cepo is available from https://pyanglab.github.io/Cepo/.
The Bioconductor package page is available from https://bioconductor.org/packages/Cepo/.
If you use Cepo in your work, please cite:
Kim, H. J., Wang, K., Chen, C., Lin, Y., Tam, P. P. L., Lin, D. M., Yang, J. Y. H. & Yang, P. Uncovering cell identity through differential stability with Cepo. Nature Computational Science 1, 784-790 (2021). https://doi.org/10.1038/s43588-021-00172-2
From R, you can also run:
citation("Cepo")To find all source code related to the analyses of the paper, please refer to https://github.com/PYangLab/CepoManuscript.
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)
If you have any enquiries, especially about using Cepo to analyse your data, please contact hani.kim@garvan.org.au or pengyi.yang@sydney.edu.au. We actively welcome any feedback and suggestions!