AddAzimuthResults | Add Azimuth Results |
AddAzimuthScores | Add Azimuth Scores |
AddModuleScore | Calculate module scores for feature expression programs in... |
AggregateExpression | Aggregated feature expression by identity class |
AnchorSet-class | The AnchorSet Class |
AnnotateAnchors | Add info to anchor matrix |
as.CellDataSet | Convert objects to CellDataSet objects |
Assay-class | The Assay Class |
as.Seurat | Convert objects to 'Seurat' objects |
as.SingleCellExperiment | Convert objects to SingleCellExperiment objects |
as.sparse | Cast to Sparse |
AugmentPlot | Augments ggplot2-based plot with a PNG image. |
AutoPointSize | Automagically calculate a point size for ggplot2-based... |
AverageExpression | Averaged feature expression by identity class |
BarcodeInflectionsPlot | Plot the Barcode Distribution and Calculated Inflection... |
BGTextColor | Determine text color based on background color |
BridgeCellsRepresentation | Construct a dictionary representation for each unimodal... |
BridgeReferenceSet-class | The BridgeReferenceSet Class The BridgeReferenceSet is an... |
BuildClusterTree | Phylogenetic Analysis of Identity Classes |
BuildNicheAssay | Construct an assay for spatial niche analysis |
CalcDispersion | Calculate dispersion of features |
CalcPerturbSig | Calculate a perturbation Signature |
CalculateBarcodeInflections | Calculate the Barcode Distribution Inflection |
CaseMatch | Match the case of character vectors |
CCAIntegration | Seurat-CCA Integration |
cc.genes | Cell cycle genes |
cc.genes.updated.2019 | Cell cycle genes: 2019 update |
CellCycleScoring | Score cell cycle phases |
Cells | Get Cell Names |
CellsByImage | Get a vector of cell names associated with an image (or set... |
CellScatter | Cell-cell scatter plot |
CellSelector | Cell Selector |
CollapseEmbeddingOutliers | Move outliers towards center on dimension reduction plot |
CollapseSpeciesExpressionMatrix | Slim down a multi-species expression matrix, when only one... |
ColorDimSplit | Color dimensional reduction plot by tree split |
CombinePlots | Combine ggplot2-based plots into a single plot |
contrast-theory | Get the intensity and/or luminance of a color |
CountSketch | Generate CountSketch random matrix |
CreateCategoryMatrix | Create one hot matrix for a given label |
CreateSCTAssayObject | Create a SCT Assay object |
CustomDistance | Run a custom distance function on an input data matrix |
CustomPalette | Create a custom color palette |
DEenrichRPlot | DE and EnrichR pathway visualization barplot |
DietSeurat | Slim down a Seurat object |
DimHeatmap | Dimensional reduction heatmap |
DimPlot | Dimensional reduction plot |
DimReduc-class | The DimReduc Class |
DiscretePalette | Discrete colour palettes from pals |
DISP | Find variable features based on dispersion |
DoHeatmap | Feature expression heatmap |
DotPlot | Dot plot visualization |
ElbowPlot | Quickly Pick Relevant Dimensions |
ExpMean | Calculate the mean of logged values |
ExpSD | Calculate the standard deviation of logged values |
ExpVar | Calculate the variance of logged values |
FastRowScale | Scale and/or center matrix rowwise |
FastRPCAIntegration | Perform integration on the joint PCA cell embeddings. |
FeaturePlot | Visualize 'features' on a dimensional reduction plot |
FeatureScatter | Scatter plot of single cell data |
FetchResiduals | Calculate pearson residuals of features not in the scale.data |
FetchResidualSCTModel | Calculate pearson residuals of features not in the scale.data... |
FetchResiduals_reference | temporal function to get residuals from reference |
FilterSlideSeq | Filter stray beads from Slide-seq puck |
FindAllMarkers | Gene expression markers for all identity classes |
FindBridgeAnchor | Find bridge anchors between two unimodal datasets |
FindBridgeIntegrationAnchors | Find integration bridge anchors between query and extended... |
FindBridgeTransferAnchors | Find bridge anchors between query and extended... |
FindClusters | Cluster Determination |
FindConservedMarkers | Finds markers that are conserved between the groups |
FindIntegrationAnchors | Find integration anchors |
FindMarkers | Gene expression markers of identity classes |
FindMultiModalNeighbors | Construct weighted nearest neighbor graph |
FindNeighbors | (Shared) Nearest-neighbor graph construction |
FindSpatiallyVariableFeatures | Find spatially variable features |
FindSubCluster | Find subclusters under one cluster |
FindTransferAnchors | Find transfer anchors |
FindVariableFeatures | Find variable features |
FoldChange | Fold Change |
fortify-Spatial | Prepare Coordinates for Spatial Plots |
GaussianSketch | Gaussian sketching |
GetAssay | Get an Assay object from a given Seurat object. |
GetImage | Get Image Data |
GetIntegrationData | Get integration data |
GetResidual | Calculate pearson residuals of features not in the scale.data |
GetTissueCoordinates | Get Tissue Coordinates |
GetTransferPredictions | Get the predicted identity |
Graph-class | The Graph Class |
GroupCorrelation | Compute the correlation of features broken down by groups... |
GroupCorrelationPlot | Boxplot of correlation of a variable (e.g. number of UMIs)... |
HarmonyIntegration | Harmony Integration |
HoverLocator | Hover Locator |
HTODemux | Demultiplex samples based on data from cell 'hashing' |
HTOHeatmap | Hashtag oligo heatmap |
HVFInfo.SCTAssay | Get Variable Feature Information |
IFeaturePlot | Visualize features in dimensional reduction space... |
ImageDimPlot | Spatial Cluster Plots |
ImageFeaturePlot | Spatial Feature Plots |
IntegrateData | Integrate data |
IntegrateEmbeddings | Integrate low dimensional embeddings |
IntegrateLayers | Integrate Layers |
IntegrationAnchorSet-class | The IntegrationAnchorSet Class |
IntegrationData-class | The IntegrationData Class |
ISpatialDimPlot | Visualize clusters spatially and interactively |
ISpatialFeaturePlot | Visualize features spatially and interactively |
JackStraw | Determine statistical significance of PCA scores. |
JackStrawData-class | The JackStrawData Class |
JackStrawPlot | JackStraw Plot |
JointPCAIntegration | Seurat-Joint PCA Integration |
L2CCA | L2-Normalize CCA |
L2Dim | L2-normalization |
LabelClusters | Label clusters on a ggplot2-based scatter plot |
LabelPoints | Add text labels to a ggplot2 plot |
LeverageScore | Leverage Score Calculation |
LinkedPlots | Visualize spatial and clustering (dimensional reduction) data... |
Load10X_Spatial | Load a 10x Genomics Visium Spatial Experiment into a 'Seurat'... |
LoadAnnoyIndex | Load the Annoy index file |
LoadCurioSeeker | Load Curio Seeker data |
LoadSTARmap | Load STARmap data |
LocalStruct | Calculate the local structure preservation metric |
LogNormalize | Normalize Raw Data |
LogVMR | Calculate the variance to mean ratio of logged values |
MappingScore | Metric for evaluating mapping success |
MapQuery | Map query cells to a reference |
merge.SCTAssay | Merge SCTAssay objects |
MetaFeature | Aggregate expression of multiple features into a single... |
MinMax | Apply a ceiling and floor to all values in a matrix |
MixingMetric | Calculates a mixing metric |
MixscapeHeatmap | Differential expression heatmap for mixscape |
MixscapeLDA | Linear discriminant analysis on pooled CRISPR screen data. |
ModalityWeights-class | The ModalityWeights Class |
MULTIseqDemux | Demultiplex samples based on classification method from... |
MVP | Find variable features based on mean.var.plot |
Neighbor-class | The Neighbor Class |
NNPlot | Highlight Neighbors in DimPlot |
NNtoGraph | Convert Neighbor class to an asymmetrical Graph class |
NormalizeData | Normalize Data |
PCASigGenes | Significant genes from a PCA |
PercentAbove | Calculate the percentage of a vector above some threshold |
PercentageFeatureSet | Calculate the percentage of all counts that belong to a given... |
PlotClusterTree | Plot clusters as a tree |
PlotPerturbScore | Function to plot perturbation score distributions. |
PolyDimPlot | Polygon DimPlot |
PolyFeaturePlot | Polygon FeaturePlot |
PredictAssay | Predict value from nearest neighbors |
PrepareBridgeReference | Prepare the bridge and reference datasets |
PrepLDA | Function to prepare data for Linear Discriminant Analysis. |
PrepSCTFindMarkers | Prepare object to run differential expression on SCT assay... |
PrepSCTIntegration | Prepare an object list normalized with sctransform for... |
ProjectCellEmbeddings | Project query data to the reference dimensional reduction |
ProjectData | Project full data to the sketch assay |
ProjectDim | Project Dimensional reduction onto full dataset |
ProjectDimReduc | Project query data to reference dimensional reduction |
ProjectIntegration | Integrate embeddings from the integrated sketched.assay |
ProjectUMAP | Project query into UMAP coordinates of a reference |
PseudobulkExpression | Pseudobulk Expression |
Radius | Get Spot Radius |
Read10X | Load in data from 10X |
Read10X_Coordinates | Load 10X Genomics Visium Tissue Positions |
Read10X_h5 | Read 10X hdf5 file |
Read10X_Image | Load a 10X Genomics Visium Image |
Read10X_probe_metadata | Read10x Probe Metadata |
Read10X_ScaleFactors | Load 10X Genomics Visium Scale Factors |
ReadAkoya | Read and Load Akoya CODEX data |
ReadMtx | Load in data from remote or local mtx files |
ReadNanostring | Read and Load Nanostring SMI data |
ReadParseBio | Read output from Parse Biosciences |
ReadSlideSeq | Load Slide-seq spatial data |
ReadSTARsolo | Read output from STARsolo |
ReadVitessce | Read Data From Vitessce |
ReadVizgen | Read and Load MERFISH Input from Vizgen |
ReadXenium | Read and Load 10x Genomics Xenium in-situ data |
reexports | Objects exported from other packages |
RegroupIdents | Regroup idents based on meta.data info |
RelativeCounts | Normalize raw data to fractions |
RenameCells | Rename Cells in an Object |
RidgePlot | Single cell ridge plot |
RPCAIntegration | Seurat-RPCA Integration |
RunCCA | Perform Canonical Correlation Analysis |
RunGraphLaplacian | Run Graph Laplacian Eigendecomposition |
RunICA | Run Independent Component Analysis on gene expression |
RunLDA | Run Linear Discriminant Analysis |
RunMarkVario | Run the mark variogram computation on a given position matrix... |
RunMixscape | Run Mixscape |
RunMoransI | Compute Moran's I value. |
RunPCA | Run Principal Component Analysis |
RunSLSI | Run Supervised Latent Semantic Indexing |
RunSPCA | Run Supervised Principal Component Analysis |
RunTSNE | Run t-distributed Stochastic Neighbor Embedding |
RunUMAP | Run UMAP |
SampleUMI | Sample UMI |
SaveAnnoyIndex | Save the Annoy index |
ScaleData | Scale and center the data. |
ScaleFactors | Get image scale factors |
ScoreJackStraw | Compute Jackstraw scores significance. |
SCTAssay-class | The SCTModel Class |
SCTransform | Perform sctransform-based normalization |
SCTResults | Get SCT results from an Assay |
SelectIntegrationFeatures | Select integration features |
SelectIntegrationFeatures5 | Select integration features |
SelectSCTIntegrationFeatures | Select SCT integration features |
SetIntegrationData | Set integration data |
SetQuantile | Find the Quantile of Data |
Seurat-class | The Seurat Class |
SeuratCommand-class | The SeuratCommand Class |
Seurat-package | Seurat: Tools for Single Cell Genomics |
SeuratTheme | Seurat Themes |
SingleCorPlot | A single correlation plot |
SingleDimPlot | Plot a single dimension |
SingleExIPlot | Plot a single expression by identity on a plot |
SingleImageMap | A single heatmap from base R using 'image' |
SingleImagePlot | Single Spatial Plot |
SingleRasterMap | A single heatmap from ggplot2 using geom_raster |
SingleSpatialPlot | Base plotting function for all Spatial plots |
SketchData | Sketch Data |
SlideSeq-class | The SlideSeq class |
SpatialImage-class | The SpatialImage Class |
SpatialPlot | Visualize spatial clustering and expression data. |
SplitObject | Splits object into a list of subsetted objects. |
STARmap-class | The STARmap class |
subset.AnchorSet | Subset an AnchorSet object |
SubsetByBarcodeInflections | Subset a Seurat Object based on the Barcode Distribution... |
TopCells | Find cells with highest scores for a given dimensional... |
TopFeatures | Find features with highest scores for a given dimensional... |
TopNeighbors | Get nearest neighbors for given cell |
TransferAnchorSet-class | The TransferAnchorSet Class |
TransferData | Transfer data |
TransferSketchLabels | Transfer data from sketch data to full data |
UnSketchEmbeddings | Transfer embeddings from sketched cells to the full data |
UpdateSCTAssays | Update pre-V4 Assays generated with SCTransform in the Seurat... |
UpdateSymbolList | Get updated synonyms for gene symbols |
VariableFeaturePlot | View variable features |
VisiumV1-class | The VisiumV1 class |
VisiumV2-class | The VisiumV2 class |
VizDimLoadings | Visualize Dimensional Reduction genes |
VlnPlot | Single cell violin plot |
VST | Variance Stabilizing Transformation |
writing-integration | Writing Integration Method Functions |
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