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cff-version: 1.2.0
message: 'To cite package "scPOEM" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'scPOEM: Single-Cell Meta-Path Based Omic Embedding'
version: 0.1.2
doi: 10.32614/CRAN.package.scPOEM
abstract: 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,
  'scPOEM' 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'.
authors:
- family-names: Hou
  given-names: Yuntong
  email: houyt223@gmail.com
  orcid: https://orcid.org/0009-0005-0587-4692
- family-names: Zhong
  given-names: Yan
  email: yzhong@fem.ecnu.edu.cn
  orcid: https://orcid.org/0000-0003-2412-043X
repository: https://houyt23.r-universe.dev
commit: 67b45f44b704f54dc60d2c86a8bb8f4b11ef4ceb
date-released: '2025-09-18'
contact:
- family-names: Hou
  given-names: Yuntong
  email: houyt223@gmail.com
  orcid: https://orcid.org/0009-0005-0587-4692