scPOEM
Single-Cell Meta-Path Based Omic Embedding
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.
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CRAN Check Status
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | ERROR |
| r-oldrel-macos-x86_64 | ERROR |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | ERROR |
| r-release-macos-x86_64 | ERROR |
| r-release-windows-x86_64 | ERROR |
Check details (5 non-OK)
package dependencies
Packages required but not available: 'monocle', 'cicero' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Packages required but not available: 'monocle', 'cicero' Packages required and available but unsuitable versions: 'Biobase', 'BiocGenerics' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Packages required but not available: 'monocle', 'cicero' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Packages required but not available: 'monocle', 'cicero' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
whether package can be installed
Installation failed. See 'd:/Rcompile/CRANpkg/local/4.5/scPOEM.Rcheck/00install.out' for details.
Additional Issues
Check History
ERROR 7 OK · 0 NOTE · 0 WARNING · 7 ERROR · 0 FAILURE Mar 10, 2026
whether package can be installed
Installation failed. See 'd:/Rcompile/CRANpkg/local/4.6/scPOEM.Rcheck/00install.out' for details.
package dependencies
Packages required but not available: 'monocle', 'cicero' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Packages required but not available: 'monocle', 'cicero' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
whether package can be installed
Installation failed. See 'd:/Rcompile/CRANpkg/local/4.5/scPOEM.Rcheck/00install.out' for details.
package dependencies
Packages required but not available: 'monocle', 'cicero' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Packages required but not available: 'monocle', 'cicero' Packages required and available but unsuitable versions: 'Biobase', 'BiocGenerics' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
whether package can be installed
Installation failed. See 'd:/Rcompile/CRANpkg/local/4.4/scPOEM.Rcheck/00install.out' for details.