Package: scPOEM
Type: Package
Title: Single-Cell Meta-Path Based Omic Embedding
Version: 0.1.3
Authors@R: c(person(given = "Yuntong", family = "Hou", email = "houyt223@gmail.com", role = c("aut","cre"), comment = c(ORCID = '0009-0005-0587-4692')),
             person(given = "Yan", family = "Zhong", email = "yzhong@fem.ecnu.edu.cn", role = c("aut","ctb"), comment = c(ORCID = '0000-0003-2412-043X')),
             person(given = "Yeran", family = "Chen", email = "yiyi0805@163.com", role = c("ctb")),
             person(given = "Youshi", family = "Chang", email = "18221126383@163.com", role = c("ctb")),
             person(given = "Yongjian", family = "Yang", email = "yjyang027@tamu.edu", role = c("ctb"), comment = c(ORCID = '0000-0002-4135-5014')),
             person(given = "Xinyue", family = "Zheng", email = "10235001419@stu.ecnu.edu.cn", role = c("ctb")),
             person(given = "James", family = "Cai", email = "jcai@tamu.edu", role = c("ctb"), comment = c(ORCID = '0000-0002-8081-6725')))
Author: Yuntong Hou [aut, cre] (ORCID: <https://orcid.org/0009-0005-0587-4692>),
  Yan Zhong [aut, ctb] (ORCID: <https://orcid.org/0000-0003-2412-043X>),
  Yeran Chen [ctb],
  Youshi Chang [ctb],
  Yongjian Yang [ctb] (ORCID: <https://orcid.org/0000-0002-4135-5014>),
  Xinyue Zheng [ctb],
  James Cai [ctb] (ORCID: <https://orcid.org/0000-0002-8081-6725>)
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'. See <doi:10.1093/bioinformatics/btaf483> for more details.
URL: https://github.com/Houyt23/scPOEM
BugReports: https://github.com/Houyt23/scPOEM/issues
License: GPL (>= 2)
Encoding: UTF-8
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)
Depends: R (>= 4.1.0)
RoxygenNote: 7.3.2
NeedsCompilation: no
Packaged: 2025-09-25 06:08:15 UTC; qingzhi
Maintainer: Yuntong Hou <houyt223@gmail.com>
Repository: CRAN
Date/Publication: 2025-09-25 07:10:02 UTC
Built: R 4.6.0; ; 2025-11-13 04:01:54 UTC; windows
