Man pages for BlishLab/scriabin
Single-cell resolved interaction analysis through binning
| AlignDatasets | Align Datasets through binning |
| AssembleInteractionGraphs | Title |
| BinAnnotationPlot | Heatmap of bin-annotation overlap |
| BinCompositionAnalysis | Plot composition of each bin |
| BinDatasets | Align Datasets through binning |
| BinPostHoc | Perform post-hoc analysis of perturbed bins |
| BuildCompHeatmap | Title |
| BuildGranHeatmap | Title |
| BuildPriorInteraction | Build unweighted summarized interaction graph |
| BuildRVHeatmap | Title |
| BuildSingleHeatmap | Title |
| BuildVarianceHeatmap | Title |
| BuildWeightedInteraction | Build summarized interaction graph weighted by predicted... |
| BuildWeightedInteraction_test | Title |
| CCIMFeaturePlot | Title |
| check_completion | Helper function to check completion of bins |
| crGeneSig | Create single-cell gene signature |
| elbow | Detect Inflection Point of a Concave Curve (Elbox Method).... |
| ExploreClusters | Title |
| ExploreInteractome | Title |
| FindAllCircuits | Find all circuits in a multi-timepoint longitudinal dataset |
| FindAllInteractionPrograms | Find all interaction programs in a multi-sample dataset |
| FindCircuits | Identify circuits between two timepoints |
| FormatCircuits | Stitch multi-timepoint circuits together |
| GenerateCCIM | Calculate cell-cell interaction matrix |
| GenerateCellSignature | Generate single-cell gene signature for ligand activity... |
| GenerateInteractome | Title |
| GeneratePrioritizedInteractome | Title |
| grapes-notin-grapes | Convenient negation |
| HighlightSR | Title |
| IDPotentialLigands | Identify potential ligands for ligand activity prediction |
| IDVariantGenes | Identify genes variable across axis of interest |
| InteractionPrograms | Discover co-expressed ligand-receptor interaction programs |
| InteractionProgramSignificance | Test Interaction program statistical significance |
| IPCellTypeSummary | Identify most highly expressed interaction programs by cell... |
| IPFeaturePlot | Plot expression of interaction programs |
| LoadLR | Load ligand-receptor database |
| load_nichenet_database | Load NicheNet Database |
| LoadRawLR | Load unformatted ligand-receptor database |
| MapMetaData | Map metadata from Seurat object to CCIM object |
| mapvalues | Mapvalues (ripped from plyr) |
| PearsonDist | Plot Pearson distributions for ligand activities |
| PerturbedBins | Identify most perturbed bins across >2 samples |
| PerturbedBinSummary | Summary plots of perturbed bins |
| PlotAlluvium | Title |
| PlotAlluviumLigRec | Title |
| PlotAlluviumLT | Plot Alluvial of ligand-target links |
| PlotAlluvium_nocells | Title |
| PlotLigandTargetAlluvium | Plot connections between ligands and predicted target genes... |
| PrioritizeInteractome | Title |
| PrioritizeLigands | Title |
| random_connectivity_test | Test bin connectivity |
| RankActiveLigands | Predict ligand activity using cell-resolved gene signatures |
| RankLigandTargets | Predict ligand activity using cell-resolved gene signatures |
| resample | Resampling |
| scInteraction | Title |
| ScoreBins | Assign quality scores to each bin |
| ScoreInteractionPrograms | Score expression of single-cells by expression of discovered... |
| TopLigandsByIdent | Plot most active ligands in receiver cell type |
