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.

Installation

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.

Documentation

The documentation for Cepo is available from https://pyanglab.github.io/Cepo/.

The Bioconductor package page is available from https://bioconductor.org/packages/Cepo/.

Citing 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.

Developers

The following individuals were involved in developing the Cepo package:

Contact us

If you have any enquiries, especially about using Cepo to analyse your data, please contact or . We actively welcome any feedback and suggestions!