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scPOEM
View on CRAN: Click
here
Download and install scPOEM package within the R console
Install from CRAN:
install.packages("scPOEM")
Install from Github:
library("remotes")
install_github("cran/scPOEM") Install by package version:
library("remotes")
install_version("scPOEM", "0.1.3") Attach the package and use:
library("scPOEM")
Maintained by
Yuntong Hou
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2025-08-28
Latest Update: 2025-08-28
Description:
Provide a workflow to jointly embed chromatin accessibility peaks and expressed genes into a shared low-dimensional space using paired single-cell ATAC-seq (scATAC-seq) and single-cell RNA-seq (scRNA-seq) data. It integrates regulatory relationships among peak-peak interactions (via 'Cicero'), peak-gene interactions (via Lasso, random forest, and XGBoost), and gene-gene interactions (via principal component regression). With the input of paired scATAC-seq and scRNA-seq data matrices, it assigns a low-dimensional feature vector to each gene and peak. Additionally, it supports the reconstruction of gene-gene network with low-dimensional projections (via epsilon-NN) and then the comparison of the networks of two conditions through manifold alignment implemented in 'scTenifoldNet'.
How to cite:
Yuntong Hou (2025). scPOEM: Single-Cell Meta-Path Based Omic Embedding. R package version 0.1.3, https://cran.r-project.org/web/packages/scPOEM. Accessed 26 Aug. 2026.
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