Introduction | Parameter Tuning | Gamma Value (Metacell Aggregation) | Alpha Value (Learning Rate) | Hamming Threshold | Association Methods | Pearson Correlation (Default) | Spearman Correlation | Principal Component Regression (pcNet) | Comparison | Working with Seurat Objects | Filtering and Preprocessing | Filter Low-Expression Genes | Custom Gene Filtering | Parallel Processing | Output Analysis | Network Comparison | Differential Network Analysis | Best Practices | 1. Data Quality | 2. Prior Network Selection | 3. Parameter Selection | 4. Reproducibility | Session Information
This package is considered a duplicate. The official version of this package is found at:https://kuijjerlab.r-universe.dev/SCORPION
Package: SCORPION 1.2.2
SCORPION: Single Cell Oriented Reconstruction of PANDA Individual Optimized Networks
Constructs gene regulatory networks from single-cell gene expression data using the PANDA (Passing Attributes between Networks for Data Assimilation) algorithm.
Authors:
SCORPION_1.2.2.tar.gz
SCORPION_1.2.2.zip(r-4.7-x86_64)SCORPION_1.2.2.zip(r-4.7-arm64)SCORPION_1.2.2.zip(r-4.6-x86_64)SCORPION_1.2.2.zip(r-4.6-arm64)SCORPION_1.2.2.zip(r-4.5-x86_64)
SCORPION_1.2.2.tgz(r-4.6-x86_64)SCORPION_1.2.2.tgz(r-4.6-arm64)SCORPION_1.2.2.tgz(r-4.5-x86_64)SCORPION_1.2.2.tgz(r-4.5-arm64)
SCORPION_1.2.2.tar.gz(r-4.7-arm64)SCORPION_1.2.2.tar.gz(r-4.7-x86_64)SCORPION_1.2.2.tar.gz(r-4.6-arm64)SCORPION_1.2.2.tar.gz(r-4.6-x86_64)
SCORPION_1.2.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
SCORPION/json (API)
| # Install 'SCORPION' in R: |
| install.packages('SCORPION', repos = c('https://zaoqu-liu.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/zaoqu-liu/scorpion/issues
Pkgdown/docs site:https://zaoqu-liu.github.io
Uses libs:
Datasets:
- scorpionTest - Example single-cell gene expression, motif, and ppi data
Last updated from:c01e59eb2e (on main). Checks:15 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 188 | ||
| linux-devel-x86_64 | OK | 216 | ||
| source / vignettes | OK | 374 | ||
| linux-release-arm64 | OK | 174 | ||
| linux-release-x86_64 | OK | 194 | ||
| macos-release-arm64 | OK | 114 | ||
| macos-release-x86_64 | OK | 240 | ||
| macos-oldrel-arm64 | OK | 155 | ||
| macos-oldrel-x86_64 | OK | 248 | ||
| windows-devel-arm64 | OK | 249 | ||
| windows-devel-x86_64 | OK | 213 | ||
| windows-release-arm64 | OK | 243 | ||
| windows-release-x86_64 | OK | 180 | ||
| windows-oldrel-x86_64 | OK | 147 | ||
| wasm-release | OK | 172 |
Exports:scorpion
Dependencies:clicpp11glueigraphirlbalatticelifecyclemagrittrMatrixpbapplypkgconfigRANNRcppRcppArmadillorlangvctrs
Advanced Usage and Best Practices
Last update: 2026-01-29
Started: 2026-01-29
Algorithm and Mathematical Framework
Overview | The PANDA Algorithm | Core Concept | Mathematical Formulation | 1. Tanimoto Similarity | 2. Network Update Rules | Convergence Criterion | Metacell Aggregation | The Sparsity Problem | Solution: Metacells | Gamma Parameter | Network Normalization | Double Z-score Normalization | Computational Complexity | References | Session Information
Last update: 2026-01-29
Started: 2026-01-29
Network Visualization
Introduction | Running SCORPION | Network Statistics Visualization | Edge Weight Distribution | TF Targeting Statistics | Heatmap Visualization | Regulatory Network Heatmap | TF Cooperation Heatmap | Network Graph Visualization | Building igraph Network | Network Layout and Plotting | Subnetwork for Specific TF | Circular Network Plot | Network Centrality Analysis | Exporting Networks | Export to Cytoscape | Export to GraphML | Summary | Session Information
Last update: 2026-01-29
Started: 2026-01-29
Quick Start Guide
Introduction | Installation | Loading the Package | Example Data | Running SCORPION | Output Structure | Extracting Top Regulatory Edges | Visualizing Network Statistics | Session Information
Last update: 2026-01-29
Started: 2026-01-29
