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 |