In PYangLab/Cepo: Cepo for the identification of differentially stable genes

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:

# install.packages("remotes")
remotes::install_github("PYangLab/Cepo")

You can install the Bioconductor version of Cepo from:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("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 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:.

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
• @kevinwang09
• @PYangLab

Contact us

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

PYangLab/Cepo documentation built on June 29, 2024, 7:16 p.m.