Package: scNPM 1.0.6

Tao Liu
scNPM: Single-Cell Network Propensity Matching
Estimates and compares heterogeneous gene conditional-dependence networks from single-cell expression data. A latent Gaussian mixture and probit observation mechanism represent cellular heterogeneity and zero observations. Protein interaction information supplies edge-specific prior weights, while network propensity matching links cell clusters across conditions and guides adaptation. Staged inference freezes stable matching, disables feedback, and retains baseline-model samples for posterior group and directional differential edge selection. Functions assess balance, record criterion diagnostics, and visualize within-condition and differential networks.
Authors:
scNPM_1.0.6.tar.gz
scNPM_1.0.6.zip(r-4.7-x86_64)scNPM_1.0.6.zip(r-4.7-arm64)scNPM_1.0.6.zip(r-4.6-x86_64)scNPM_1.0.6.zip(r-4.6-arm64)
scNPM_1.0.6.tar.gz(r-4.7-arm64)scNPM_1.0.6.tar.gz(r-4.7-x86_64)scNPM_1.0.6.tar.gz(r-4.6-arm64)scNPM_1.0.6.tar.gz(r-4.6-x86_64)
scNPM_1.0.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scNPM/json (API)
| # Install 'scNPM' in R: |
| install.packages('scNPM', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/taostat1/scnpm_r_package/issues
- cell - Cell-Level Metadata
- cols_to_MR - Column Indices of MR Cells
- cols_to_PR - Column Indices of PR Cells
- goal_gene - Target Gene Names
- goal_gene_mt - Top-50 Gene Expression Matrix
- mt - Full Gene Expression Matrix
Last updated from:44d9b4a0a6. Checks:10 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 167 | ||
| linux-devel-x86_64 | OK | 147 | ||
| source / vignettes | OK | 236 | ||
| linux-release-arm64 | OK | 129 | ||
| linux-release-x86_64 | OK | 168 | ||
| windows-devel-arm64 | OK | 243 | ||
| windows-devel-x86_64 | OK | 197 | ||
| windows-release-arm64 | OK | 410 | ||
| windows-release-x86_64 | OK | 227 | ||
| wasm-release | OK | 123 |
Exports:compute_qf_smdplot_diff_networkplot_group_networkrun_scNPMselect_differential_edgesselect_group_edges
Dependencies:clicpp11farverggplot2ggrepelgluegtableigraphisobandlabelinglatticelifecyclemagrittrMatrixpkgconfigR6RColorBrewerRcppRcppArmadilloRcppParallelrlangS7scalesvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Cell-Level Metadata (AMD Example Data) | cell |
| Column Indices of MR Cells (AMD Example Data) | cols_to_MR |
| Column Indices of PR Cells (AMD Example Data) | cols_to_PR |
| Compute the SMD of the Network Quadratic Form for Matched Cluster Pairs | compute_qf_smd |
| Target Gene Names (AMD Example Data) | goal_gene |
| Top-50 Gene Expression Matrix (AMD Example Data) | goal_gene_mt |
| Full Gene Expression Matrix (AMD Example Data) | mt |
| Plot Differential Gene Regulatory Network (Combined/Separate Mode) | plot_diff_network |
| Plot a Selected Group Network | plot_group_network |
| Run Single-Cell Network Propensity Matching (scNPM) | run_scNPM |
| Select Differential Edges by Posterior Directional Error | select_differential_edges |
| Select Group Networks by Posterior Expected False Discovery Proportion | select_group_edges |