scPOEM: Single-Cell Meta-Path Based Omic Embedding

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'.

Version:	0.1.2
Depends:	R (≥ 4.1.0)
Imports:	methods, utils, stats, foreach (≥ 1.5.2), doParallel (≥ 1.0.17), tictoc (≥ 1.2.1), Matrix (≥ 1.6-3), glmnet (≥ 4.1-8), xgboost (≥ 1.7.10), reticulate, stringr, magrittr, scTenifoldNet, VGAM (≥ 1.1-13), Biobase (≥ 2.66.0), BiocGenerics (≥ 0.52.0), monocle (≥ 2.34.0), cicero (≥ 1.24.0)
Published:	2025-08-28
DOI:	10.32614/CRAN.package.scPOEM
Author:	Yuntong Hou [aut, cre], Yan Zhong [aut, ctb], Yongjian Yang [ctb], Xinyue Zheng [ctb], James Cai [ctb], Yeran Chen [ctb], Youshi Chang [ctb]
Maintainer:	Yuntong Hou <houyt223 at gmail.com>
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation:	no
CRAN checks:	scPOEM results

Documentation:

Reference manual:

scPOEM.html , scPOEM.pdf

Downloads:

Package source:	scPOEM_0.1.2.tar.gz
Windows binaries:	r-devel: scPOEM_0.1.2.zip, r-release: not available, r-oldrel: scPOEM_0.1.2.zip
macOS binaries:	r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available

Linking:

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