Seurat : R toolkit for single cell genomics

AddImputedScore | Calculate imputed expression values |

AddMetaData | Add Metadata |

AddSamples | Add samples into existing Seurat object. |

AddSmoothedScore | Calculate smoothed expression values |

AssessNodes | Assess Internal Nodes |

AssessSplit | Assess Cluster Split |

AverageExpression | Averaged gene expression by identity class |

AveragePCA | Average PCA scores by identity class |

BatchGene | Identify potential genes associated with batch effects |

BuildClusterTree | Phylogenetic Analysis of Identity Classes |

BuildRFClassifier | Build Random Forest Classifier |

BuildSNN | SNN Graph Construction |

CellPlot | Cell-cell scatter plot |

ClassifyCells | Classify New Data |

ClusterAlpha | Probability of detection by identity class |

ColorTSNESplit | Color tSNE Plot Based on Split |

DBClustDimension | Perform spectral density clustering on single cells |

DiffExpTest | Likelihood ratio test for zero-inflated data |

DiffTTest | Differential expression testing using Student's t-test |

DimPlot | Dimensional reduction plot |

DoHeatmap | Gene expression heatmap |

DoKMeans | K-Means Clustering |

DotPlot | Dot plot visualization |

FeatureHeatmap | Vizualization of multiple features |

FeaturePlot | Visualize 'features' on a dimensional reduction plot |

FetchData | Access cellular data |

FindAllMarkers | Gene expression markers for all identity classes |

FindAllMarkersNode | Find all markers for a node |

FindClusters | Cluster Determination |

FindMarkers | Gene expression markers of identity classes |

FindMarkersNode | Gene expression markers of identity classes defined by a... |

FitGeneK | Build mixture models of gene expression |

GenePlot | Scatter plot of single cell data |

GetCentroids | Get cell centroids |

HeatmapNode | Node Heatmap |

ICA | Run Independent Component Analysis on gene expression |

ICAPlot | Plot ICA map |

ICHeatmap | Independent component heatmap |

ICTopGenes | Find genes with highest ICA scores |

InitialMapping | Infer spatial origins for single cells |

JackStraw | Determine statistical significance of PCA scores. |

JackStrawPlot | JackStraw Plot |

KClustDimension | Perform spectral k-means clustering on single cells |

LogNormalize | Normalize raw data |

MakeSparse | Make object sparse |

MarkerTest | ROC-based marker discovery |

MeanVarPlot | Identify variable genes |

MergeNode | Merge subchilden of a node |

MergeSeurat | Merge Seurat Objects |

NegBinomDETest | Negative binomial test for UMI-count based data |

PCA | Run Principal Component Analysis on gene expression |

PCAFast | Run Principal Component Analysis on gene expression using... |

PCAPlot | Plot PCA map |

PCASigGenes | Significant genes from a PCA |

PCElbowPlot | Quickly Pick Relevant PCs |

PCHeatmap | Principal component heatmap |

PCTopCells | Find cells with highest PCA scores |

PCTopGenes | Find genes with highest PCA scores |

PlotClusterTree | Plot phylogenetic tree |

PlotNoiseModel | Visualize expression/dropout curve |

PoissonDETest | Poisson test for UMI-count based data |

PrintPCA | Print the results of a PCA analysis |

ProjectPCA | Project Principal Components Analysis onto full dataset |

Read10X | Load in data from 10X |

RefinedMapping | Quantitative refinement of spatial inferences |

RegressOut | Regress out technical effects and cell cycle |

RenameIdent | Rename one identity class to another |

ReorderIdent | Reorder identity classes |

RunDiffusion | Run t-distributed Stochastic Neighbor Embedding |

RunTSNE | Run t-distributed Stochastic Neighbor Embedding |

SampleUMI | Sample UMI |

ScaleData | Scale and center the data |

SetAllIdent | Switch identity class definition to another variable |

SetIdent | Set identity class information |

Setup | Setup Seurat object |

seurat | The Seurat Class |

Seurat-deprecated | Deprecated function(s) in the Seurat package |

StashIdent | Set identity class information |

SubsetCells | Return a subset of the Seurat object |

SubsetData | Return a subset of the Seurat object |

TobitTest | Differential expression testing using Tobit models |

TSNEPlot | Plot tSNE map |

ValidateClusters | Cluster Validation |

ValidateSpecificClusters | Specific Cluster Validation |

VizClassification | Highlight classification results |

VizICA | Visualize ICA genes |

VizPCA | Visualize PCA genes |

VlnPlot | Single cell violin plot |

WhichCells | Identify cells matching certain criteria |

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