Package: Connectome 1.0.2

Connectome: Single Cell Connectomics

A toolkit for exploring cell-cell connectivity patterns based on ligand and receptor expression in heterogeneous single-cell datasets. Implements methods for constructing, filtering, and visualizing connectomic networks from single-cell RNA sequencing data. Supports multiple species via the FANTOM5 ligand-receptor database. Methods described in Raredon et al (2022) <doi:10.1038/s41598-022-07959-x>.

Authors:Zaoqu Liu [aut, cre], Micha Sam Brickman Raredon [aut]

Connectome_1.0.2.tar.gz
Connectome_1.0.2.zip(r-4.7)Connectome_1.0.2.zip(r-4.6)Connectome_1.0.2.zip(r-4.5)
Connectome_1.0.2.tgz(r-4.6-any)Connectome_1.0.2.tgz(r-4.5-any)
Connectome_1.0.2.tar.gz(r-4.7-any)Connectome_1.0.2.tar.gz(r-4.6-any)
Connectome_1.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Connectome/json (API)

# Install 'Connectome' in R:
install.packages('Connectome', repos = c('https://zaoqu-liu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zaoqu-liu/connectome/issues

Pkgdown/docs site:https://zaoqu-liu.github.io

Datasets:

On CRAN:

Conda:

3.94 score 35 scripts 16 exports 157 dependencies

Last updated from:956f1e43d8 (on main). Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK405
source / vignettesOK345
linux-release-x86_64OK324
macos-release-arm64OK269
macos-oldrel-arm64OK201
windows-develOK247
windows-releaseOK267
windows-oldrelOK256
wasm-releaseOK210

Exports:CellCellScatterCentralityCircosDiffCircosPlotCompareCentralityCreateConnectomeDiffEdgeDotPlotDifferentialConnectomeDifferentialScoringPlotEdgeDotPlotEvenSplitFilterConnectomeModalDotPlotNetworkPlotSignalScatterSingleCellConnectome

Dependencies:abindaskpassbase64encBHBiocGenericsbitopsbslibcachemcaToolscirclizecliclueclustercodetoolscolorspacecommonmarkComplexHeatmapcowplotcpp11crayoncrosstalkcurldata.tabledeldirdigestdoParalleldotCall64dplyrdqrngevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomeforeachfsfuturefuture.applygenericsGetoptLongggplot2ggrepelggridgesGlobalOptionsglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemimeminiUInlmeopensslotelparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterjsonrlangrmarkdownROCRrprojrootRSpectraRtsneS4VectorsS7sassscalesscattermoresctransformSeuratSeuratObjectshapeshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxtableyamlzoo

Introduction to Connectome
Overview | Key Features | Installation | From R-universe (Recommended) | From GitHub | Quick Start | Load Required Packages | Prepare Your Data | Create Connectome | Filter Edges | Visualize Results | Network Plot | Circos Plot | Centrality Analysis | Understanding the Output | Workflow Summary | Next Steps | Citation | Session Info
Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2026-01-23
Started: 2026-01-23

Visualization Gallery
Overview | Example Data Preparation | Network Visualizations | 1. NetworkPlot | 2. CircosPlot | Dot Plot Visualizations | 3. EdgeDotPlot | Centrality Analysis | 4. Centrality | Scatter Plots | 5. SignalScatter | Customization Tips | Color Palettes | Filtering Before Plotting | Saving High-Quality Figures | Visualization Selection Guide | Session Info
Rendered fromvisualization.Rmdusingknitr::rmarkdown

Last update: 2026-01-23
Started: 2026-01-23

Algorithm Principles and Mathematical Framework
Theoretical Foundation | 1. Ligand-Receptor Database | FANTOM5 Database | Evidence Levels | 2. Edge Weight Computation | Expression Metrics | Edge Weight Functions | 3. Statistical Testing | Wilcoxon Rank-Sum Test | Multiple Testing Correction | 4. Diagnostic Odds Ratio (DOR) | Standard DOR | Haldane-Anscombe Correction | 5. Network Centrality Analysis | Graph Construction | Kleinberg's Hub and Authority Scores | 6. Differential Connectivity Analysis | Fold Change Computation | Perturbation Score | 7. Implementation Details | Computational Complexity | Memory Efficiency | References | Session Info
Rendered fromalgorithm.Rmdusingknitr::rmarkdown

Last update: 2026-01-23
Started: 2026-01-23

Best Practices and Troubleshooting
Data Preparation | Input Requirements | Preprocessing Checklist | Cell Type Considerations | Parameter Optimization | CreateConnectome Parameters | FilterConnectome Parameters | Performance Optimization | Large Datasets | Parallel Processing | Common Issues and Solutions | Issue 1: No edges after filtering | Issue 2: Missing cell types in visualization | Issue 3: Memory errors | Issue 4: Species mismatch | Issue 5: Custom ligand-receptor database | Quality Control | Sanity Checks | Biological Validation | Reproducibility | Setting Seeds | Saving Results | Session Documentation | Session Info
Rendered frombest-practices.Rmdusingknitr::rmarkdown

Last update: 2026-01-23
Started: 2026-01-23

Differential Connectivity Analysis
Overview | Workflow | Step 1: Prepare Data | Split by Condition | Why EvenSplit? | Step 2: Create Individual Connectomes | Step 3: Compute Differential Connectome | Output Columns | Step 4: Interpret Results | Perturbation Score | Example Interpretation | Step 5: Visualization | Circos Diagram | Edge Dot Plot | Scoring Heatmap | Advanced Analysis | Mode-Specific Changes | Cell Type-Specific Changes | Export Results | Best Practices | Sample Size | Filtering Strategy | Handling Infinite Values | Common Pitfalls | Session Info
Rendered fromdifferential-analysis.Rmdusingknitr::rmarkdown

Last update: 2026-01-23
Started: 2026-01-23

Readme and manuals

Help Manual

Help pageTopics
CellCellScatterCellCellScatter
CentralityCentrality
CircosDiffCircosDiff
CircosPlotCircosPlot
CompareCentralityCompareCentrality
CreateConnectomeCreateConnectome
DiffEdgeDotPlotDiffEdgeDotPlot
DifferentialConnectomeDifferentialConnectome
DifferentialScoringPlotDifferentialScoringPlot
EdgeDotPlotEdgeDotPlot
EvenSplitEvenSplit
FilterConnectomeFilterConnectome
ModalDotPlotModalDotPlot
FANTOM5 Ligand-Receptor Database (Original)ncomms8866
FANTOM5 Ligand-Receptor Database (Human)ncomms8866_human
FANTOM5 Ligand-Receptor Database (Mouse)ncomms8866_mouse
FANTOM5 Ligand-Receptor Database (Pig)ncomms8866_pig
FANTOM5 Ligand-Receptor Database (Rat)ncomms8866_rat
NetworkPlotNetworkPlot
SignalScatterSignalScatter
SingleCellConnectomeSingleCellConnectome