API for nukappa/seurat_v2
Seurat : R toolkit for single cell genomics
| Global functions | |
|---|---|
| AddImputedScore | Man page |
| AddMetaData | Man page |
| AddSamples | Man page |
| AddSmoothedScore | Man page |
| AssessNodes | Man page |
| AssessSplit | Man page |
| AverageExpression | Man page |
| AveragePCA | Man page |
| BatchGene | Man page |
| BuildClusterTree | Man page |
| BuildRFClassifier | Man page |
| BuildSNN | Man page |
| CalcConnectivity | Source code |
| CalcSNNDense | Source code |
| CalcSNNSparse | Source code |
| CellPlot | Man page |
| ClassifyCells | Man page |
| ClusterAlpha | Man page |
| ColorTSNESplit | Man page |
| DBClustDimension | Man page |
| DBclust_dimension | Man page Source code |
| DFT | Source code |
| DiffExpTest | Man page |
| DiffTTest | Man page |
| DimPlot | Man page |
| DoHeatmap | Man page |
| DoKMeans | Man page |
| DotPlot | Man page |
| FeatureHeatmap | Man page |
| FeaturePlot | Man page |
| FetchData | Man page |
| FindAllMarkers | Man page |
| FindAllMarkersNode | Man page |
| FindClusters | Man page |
| FindMarkers | Man page |
| FindMarkersNode | Man page |
| FitGeneK | Man page |
| GenePlot | Man page |
| GetAllInternalNodes | Source code |
| GetCentroids | Man page |
| GroupSingletons | Source code |
| Hbeta | Source code |
| HeatmapNode | Man page |
| ICA | Man page |
| ICAPlot | Man page |
| ICHeatmap | Man page |
| ICTopGenes | Man page |
| InitialMapping | Man page |
| JackStraw | Man page |
| JackStrawPlot | Man page |
| KClustDimension | Man page |
| Kclust_dimension | Man page Source code |
| KullbackFun | Source code |
| LogNorm | Source code |
| LogNormalize | Man page |
| MakeSparse | Man page |
| MarkerTest | Man page |
| MeanVarPlot | Man page |
| MergeNode | Man page |
| MergeSeurat | Man page |
| MultiPlotList | Source code |
| NegBinomDETest | Man page |
| NegBinomDiffExpTest | Source code |
| NodeHasChild | Source code |
| NodeHasOnlyChildren | Source code |
| PCA | Man page |
| PCAFast | Man page |
| PCAPlot | Man page |
| PCASigGenes | Man page |
| PCElbowPlot | Man page |
| PCHeatmap | Man page |
| PCTopCells | Man page |
| PCTopGenes | Man page |
| PlotClusterTree | Man page |
| PlotNoiseModel | Man page |
| PoissonDETest | Man page |
| PrintPCA | Man page |
| ProjectPCA | Man page |
| Read10X | Man page |
| RefinedMapping | Man page |
| RegressOut | Man page |
| RenameIdent | Man page |
| ReorderIdent | Man page |
| RowMergeMatrices | Source code |
| RowMergeSparseMatrices | Source code |
| RunClassifier | Source code |
| RunDiffusion | Man page |
| RunModularityClustering | Source code |
| RunTSNE | Man page |
| RunUMISampling | Source code |
| RunUMISamplingPerCell | Source code |
| SampleUMI | Man page |
| ScaleData | Man page |
| SetAllIdent | Man page |
| SetIdent | Man page |
| Setup | Man page |
| Seurat-deprecated | Man page |
| SingleFeaturePlot | Source code |
| StashIdent | Man page |
| SubsetCells | Man page |
| SubsetData | Man page |
| TSNEPlot | Man page |
| TobitDiffExpTest | Source code |
| TobitTest | Man page |
| ValidateClusters | Man page |
| ValidateSpecificClusters | Man page |
| VizClassification | Man page |
| VizICA | Man page |
| VizPCA | Man page |
| VlnPlot | Man page |
| WhichCells | Man page |
| addImputedScore | Man page Source code |
| addMetaData | Man page Source code |
| addSmoothedScore | Man page Source code |
| add_samples | Man page Source code |
| ainb | Source code |
| all.neighbor.cells | Source code |
| anotinb | Source code |
| arrange | Source code |
| auc | Source code |
| aucFxn | Source code |
| average.expression | Man page Source code |
| average.pca | Man page Source code |
| batch.gene | Man page Source code |
| bimodLikData | Source code |
| buildClusterTree | Man page Source code |
| calc.drop.prob | Source code |
| calc.insitu | Man page Source code |
| calcFP | Source code |
| calcMedians | Source code |
| calcNoiseModels | Man page Source code |
| calcResid | Source code |
| calcResidLog | Source code |
| calcTP | Source code |
| calinskiPlot | Man page Source code |
| cell.centroid | Source code |
| cell.centroid.x | Source code |
| cell.centroid.y | Source code |
| cell.cor.matrix | Man page Source code |
| cellPlot | Man page Source code |
| cluster.alpha | Man page Source code |
| compareBins | Source code |
| comparePCA | Source code |
| corCellWeightFast | Source code |
| covCellWeightFast | Source code |
| custom.dist | Source code |
| cv | Source code |
| d2p_cell | Source code |
| diff.t.test | Man page Source code |
| diffAUC | Source code |
| diffExp.test | Man page Source code |
| diffLRT | Source code |
| diffNegBinom | Source code |
| diffTobit | Source code |
| dim.plot | Man page Source code |
| doHeatMap | Man page Source code |
| doKMeans | Man page Source code |
| dot.plot | Man page Source code |
| empP | Source code |
| exact.cell.centroid | Source code |
| expAlpha | Source code Source code |
| expMean | Source code |
| expSD | Source code |
| expVar | Source code |
| extract_field | Source code |
| feature.heatmap | Man page Source code |
| feature.plot | Man page Source code |
| feature.plot.keynote | Man page Source code |
| fetch.closest | Source code |
| fetch.data | Man page Source code |
| fetch.mincells | Source code |
| find.markers | Man page Source code |
| find.markers.node | Man page Source code |
| findNGene | Source code |
| find_all_markers | Man page Source code |
| fit.gene.k | Man page Source code |
| fit.gene.mix | Man page Source code |
| genCols | Source code |
| gene.cor.matrix | Man page Source code |
| genePlot | Man page Source code |
| geneScorePlot | Man page Source code |
| genes.ca.range | Source code |
| genes.in.cluster | Man page Source code |
| get.centroids | Man page Source code |
| getAB | Source code |
| getCoefs | Source code |
| getDescendants | Source code |
| getLeftDecendants | Source code |
| getNewScore | Man page Source code |
| getRightDecendants | Source code |
| getSmooth | Source code |
| getStat | Source code |
| getStat1 | Source code |
| getStat2 | Source code |
| getStat3 | Source code |
| getWeightMatrix | Man page Source code |
| gg.legend.pts | Source code |
| gg.legend.text | Source code |
| gg.xax | Source code |
| gg.yax | Source code |
| gtCut | Source code |
| humpCt | Source code |
| humpMean | Source code |
| humpVar | Source code |
| icHeatmap | Man page Source code |
| icTopGenes | Man page Source code |
| ica | Man page Source code |
| ica.plot | Man page Source code |
| init | Source code |
| initial.mapping | Man page Source code |
| iter.k.fit | Source code |
| jackF | Source code |
| jackRandom | Source code |
| jackStraw | Man page Source code |
| jackStraw.permutation.test | Man page Source code |
| jackStrawF | Source code |
| jackStrawFull | Man page Source code |
| jackStrawMC | Man page Source code |
| jackStrawPlot | Man page Source code |
| kMeansHeatmap | Man page Source code |
| kill.ifnull | Source code |
| lasso.fxn | Source code |
| logMeanMinus | Source code |
| logVarDivMean | Source code |
| logVarMinus | Source code |
| logVarMinus2 | Source code |
| log_add | Source code |
| makeAlnPlot | Source code |
| makeScorePlot2 | Source code |
| map.cell | Man page Source code |
| map.cell.score | Source code |
| marker.auc.test | Source code |
| marker.test | Man page Source code |
| mean.var.plot | Man page Source code |
| meanNormFunction | Source code |
| meanVarPlot | Source code |
| mergeDescendents | Source code |
| minmax | Source code |
| minusc | Source code |
| minusr | Source code |
| nb.residuals | Source code |
| neighbor.cells | Source code |
| normal.sample | Source code |
| pcHeatmap | Man page Source code |
| pcTopCells | Man page Source code |
| pcTopGenes | Man page Source code |
| pca | Man page Source code |
| pca.plot | Man page Source code |
| pca.sig.genes | Man page Source code |
| plot.Vln | Source code |
| plotClusterTree | Man page Source code |
| plotNoiseModel | Man page Source code |
| plotVln | Source code |
| posterior.plot | Man page Source code |
| print.pca | Man page Source code |
| project.pca | Man page Source code |
| project.samples | Man page Source code |
| project_map | Source code |
| quickRNAHuman | Source code |
| refined.mapping | Man page Source code |
| regression.sig | Source code |
| regulatorScore | Man page Source code |
| removePC | Man page Source code |
| rename.ident | Man page Source code |
| reorder.ident | Man page Source code |
| returnTopX | Source code |
| rp | Source code |
| run_diffusion | Man page Source code |
| run_tsne | Man page Source code |
| same | Source code |
| scaleSCMatrix2 | Source code |
| sensitivityCurve | Source code |
| set.all.ident | Man page Source code |
| set.ident | Man page Source code |
| set.ifnull | Source code |
| setWt1 | Source code |
| setWtMatrix1 | Source code |
| setup | Man page Source code |
| seurat | Man page |
| seurat-class | Man page |
| shift.cell | Source code |
| shuffleMatRow | Source code |
| situ3d | Source code |
| sort.column | Source code |
| spatial.de | Man page Source code |
| sub.string | Source code |
| subSort | Source code |
| subc | Source code |
| subr | Source code |
| subsetCells | Man page Source code |
| subsetData | Man page Source code |
| tnse.plot | Man page |
| tobit.test | Man page Source code |
| tobit_fitter | Source code |
| topGenesForDim | Source code |
| translate.dim.code | Source code |
| tsne.plot | Man page Source code |
| viz.ica | Man page Source code |
| viz.pca | Man page Source code |
| vlnPlot | Man page Source code |
| vminusc | Source code |
| vp.layout | Source code |
| vsubc | Source code |
| weighted.euclidean | Source code |
| which.cells | Man page Source code |
| writ.table | Source code |
| wtCov | Source code |
| zf.anchor.map | Source code |
| zf.anchor.render | Source code |
| zf.cells.render | Source code |
| zf.insitu.dorsal | Source code |
| zf.insitu.lateral | Source code |
| zf.insitu.side | Source code |
| zf.insitu.vec.lateral | Source code |
| zf.insitu.ventral | Source code |
