The R package decemedip is a novel computational paradigm developed for inferring the relative abundances of cell types and tissues from tissue bulk or circulating cell-free DNA (cfDNA) measure by methylated DNA immunoprecipitation sequencing (MeDIP-Seq). This paradigm allows using reference data from other technologies such as microarray or WGBS.
You can install the development version of decemedip in R from
GitHub with:
# install.packages("devtools")
devtools::install_github("nshen7/decemedip")An online vignette on the decemedip package can be found at https://rpubs.com/nshen7/how-to-use-decemedip.
If you have questions or suggestions regarding the decemedip package, please feel free raise an issue in this GitHub page or alternatively email the author, Ning, at ning.shen.wk@gmail.com.
decemedip: hierarchical Bayesian modeling for cell type deconvolution of immunoprecipitation-based DNA methylomes. Ning Shen, Ze Zhang, Sylvan Baca, Keegan Korthauer. bioRxiv (2025). https://doi.org/10.1101/2025.05.09.653152