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'. See <doi:10.1093/bioinformatics/btaf483> for more details.
| Version: | 0.1.3 |
| 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: | 2025-09-25 |
| DOI: | 10.32614/CRAN.package.scPOEM |
| Author: | Yuntong Hou [aut, cre], Yan Zhong [aut, ctb], Yeran Chen [ctb], Youshi Chang [ctb], Yongjian Yang [ctb], Xinyue Zheng [ctb], James Cai [ctb] |
| Maintainer: | Yuntong Hou <houyt223 at gmail.com> |
| BugReports: | https://github.com/Houyt23/scPOEM/issues |
| License: | GPL-2 |GPL-3 [expanded from: GPL (≥ 2)] |
| URL: | https://github.com/Houyt23/scPOEM |
| NeedsCompilation: | no |
| CRAN checks: | scPOEM results |
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