calcEffectSizes | Finds the effect sizes for all genes in the original dataset,... |
combineSCE | Combine a list of SingleCellExperiment objects as one... |
computeHeatmap | Computes heatmap for a set of features against dimensionality... |
computeZScore | Compute Z-Score |
constructSCE | Create SingleCellExperiment object from csv or txt input |
convertSCEToSeurat | convertSCEToSeurat Converts sce object to seurat while... |
convertSeuratToSCE | convertSeuratToSCE Converts the input seurat object to a sce... |
dedupRowNames | Deduplicate the rownames of a matrix or SingleCellExperiment... |
detectCellOutlier | Detecting outliers within the SingleCellExperiment object. |
diffAbundanceFET | Calculate Differential Abundance with FET |
discreteColorPalette | Generate given number of color codes |
distinctColors | Generate a distinct palette for coloring different clusters |
downSampleCells | Estimate numbers of detected genes, significantly... |
downSampleDepth | Estimate numbers of detected genes, significantly... |
expData | expData Get data item from an input 'SingleCellExperiment'... |
expData-ANY-character-method | expData Get data item from an input 'SingleCellExperiment'... |
expDataNames | expDataNames Get names of all the data items in the input... |
expDataNames-ANY-method | expDataNames Get names of all the data items in the input... |
expData-set | expData Store data items using tags to identify the type of... |
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method | expData Store data items using tags to identify the type of... |
expDeleteDataTag | expDeleteDataTag Remove tag against an input data from the... |
exportSCE | Export data in SingleCellExperiment object |
exportSCEtoAnnData | Export a SingleCellExperiment R object as Python annData... |
exportSCEtoFlatFile | Export a SingleCellExperiment object to flat text files |
exportSCEToSeurat | Export data in Seurat object |
expSetDataTag | expSetDataTag Set tag to an assay or a data item in the input... |
expTaggedData | expTaggedData Returns a list of names of data items from the... |
featureIndex | Retrieve row index for a set of features |
generateHTANMeta | Generate HTAN manifest file for droplet and cell count data |
generateMeta | Generate HTAN manifest file for droplet and cell count data |
generateSimulatedData | Generates a single simulated dataset, bootstrapping from the... |
getBiomarker | Given a list of genes and a SingleCellExperiment object,... |
getDEGTopTable | Get Top Table of a DEG analysis |
getDiffAbundanceResults | Get/Set diffAbundanceFET result table |
getEnrichRResult | Get or Set EnrichR Result |
getFindMarkerTopTable | Fetch the table of top markers that pass the filtering |
getGenesetNamesFromCollection | List geneset names from geneSetCollection |
getMSigDBTable | Shows MSigDB categories |
getPathwayResultNames | List pathway analysis result names |
getSampleSummaryStatsTable | Stores and returns table of SCTK QC outputs to metadata. |
getSceParams | Extract QC parameters from the SingleCellExperiment object |
getSeuratVariableFeatures | Get variable feature names after running runSeuratFindHVG... |
getSoupX | Get or Set SoupX Result |
getTopHVG | Get or set top HVG after calculation |
getTSCANResults | getTSCANResults accessor function |
importAlevin | Construct SCE object from Salmon-Alevin output |
importAnnData | Create a SingleCellExperiment Object from Python AnnData... |
importBUStools | Construct SCE object from BUStools output |
importCellRanger | Construct SCE object from Cell Ranger output |
importCellRangerV2Sample | Construct SCE object from Cell Ranger V2 output for a single... |
importCellRangerV3Sample | Construct SCE object from Cell Ranger V3 output for a single... |
importDropEst | Create a SingleCellExperiment Object from DropEst output |
importExampleData | Retrieve example datasets |
importFromFiles | Create a SingleCellExperiment object from files |
importGeneSetsFromCollection | Imports gene sets from a GeneSetCollection object |
importGeneSetsFromGMT | Imports gene sets from a GMT file |
importGeneSetsFromList | Imports gene sets from a list |
importGeneSetsFromMSigDB | Imports gene sets from MSigDB |
importMitoGeneSet | Import mitochondrial gene sets |
importMultipleSources | Imports samples from different sources and compiles them into... |
importOptimus | Construct SCE object from Optimus output |
importSEQC | Construct SCE object from seqc output |
importSTARsolo | Construct SCE object from STARsolo outputs |
iterateSimulations | Returns significance data from a snapshot. |
listSampleSummaryStatsTables | Lists the table of SCTK QC outputs stored within the... |
mergeSCEColData | Merging colData from two singleCellExperiment objects |
MitoGenes | List of mitochondrial genes of multiple reference |
mouseBrainSubsetSCE | Example Single Cell RNA-Seq data in SingleCellExperiment... |
msigdb_table | MSigDB gene get Category table |
plotBarcodeRankDropsResults | Plots for runBarcodeRankDrops outputs. |
plotBarcodeRankScatter | Plots for runBarcodeRankDrops outputs. |
plotBatchCorrCompare | Plot comparison of batch corrected result against original... |
plotBatchVariance | Plot the percent of the variation that is explained by batch... |
plotBcdsResults | Plots for runBcds outputs. |
plotBubble | Plot Bubble plot |
plotClusterAbundance | Plot the differential Abundance |
plotCxdsResults | Plots for runCxds outputs. |
plotDecontXResults | Plots for runDecontX outputs. |
plotDEGHeatmap | Heatmap visualization of DEG result |
plotDEGRegression | Create linear regression plot to show the expression the of... |
plotDEGViolin | Generate violin plot to show the expression of top DEGs |
plotDEGVolcano | Generate volcano plot for DEGs |
plotDimRed | Plot dimensionality reduction from computed metrics including... |
plotDoubletFinderResults | Plots for runDoubletFinder outputs. |
plotEmptyDropsResults | Plots for runEmptyDrops outputs. |
plotEmptyDropsScatter | Plots for runEmptyDrops outputs. |
plotFindMarkerHeatmap | Plot a heatmap to visualize the result of 'runFindMarker' |
plotMASTThresholdGenes | MAST Identify adaptive thresholds |
plotPathway | Generate violin plots for pathway analysis results |
plotPCA | Plot PCA run data from its components. |
plotRunPerCellQCResults | Plots for runPerCellQC outputs. |
plotScanpyDotPlot | plotScanpyDotPlot |
plotScanpyEmbedding | plotScanpyEmbedding |
plotScanpyHeatmap | plotScanpyHeatmap |
plotScanpyHVG | plotScanpyHVG |
plotScanpyMarkerGenes | plotScanpyMarkerGenes |
plotScanpyMarkerGenesDotPlot | plotScanpyMarkerGenesDotPlot |
plotScanpyMarkerGenesHeatmap | plotScanpyMarkerGenesHeatmap |
plotScanpyMarkerGenesMatrixPlot | plotScanpyMarkerGenesMatrixPlot |
plotScanpyMarkerGenesViolin | plotScanpyMarkerGenesViolin |
plotScanpyMatrixPlot | plotScanpyMatrixPlot |
plotScanpyPCA | plotScanpyPCA |
plotScanpyPCAGeneRanking | plotScanpyPCAGeneRanking |
plotScanpyPCAVariance | plotScanpyPCAVariance |
plotScanpyViolin | plotScanpyViolin |
plotScDblFinderResults | Plots for runScDblFinder outputs. |
plotScdsHybridResults | Plots for runCxdsBcdsHybrid outputs. |
plotSCEBarAssayData | Bar plot of assay data. |
plotSCEBarColData | Bar plot of colData. |
plotSCEBatchFeatureMean | Plot mean feature value in each batch of a... |
plotSCEDensity | Density plot of any data stored in the SingleCellExperiment... |
plotSCEDensityAssayData | Density plot of assay data. |
plotSCEDensityColData | Density plot of colData. |
plotSCEDimReduceColData | Dimension reduction plot tool for colData |
plotSCEDimReduceFeatures | Dimension reduction plot tool for assay data |
plotSCEHeatmap | Plot heatmap of using data stored in SingleCellExperiment... |
plotSCEScatter | Dimension reduction plot tool for all types of data |
plotSCEViolin | Violin plot of any data stored in the SingleCellExperiment... |
plotSCEViolinAssayData | Violin plot of assay data. |
plotSCEViolinColData | Violin plot of colData. |
plotScrubletResults | Plots for runScrublet outputs. |
plotSeuratElbow | plotSeuratElbow Computes the plot object for elbow plot from... |
plotSeuratGenes | Compute and plot visualizations for marker genes |
plotSeuratHeatmap | plotSeuratHeatmap Modifies the heatmap plot object so it... |
plotSeuratHVG | plotSeuratHVG Plot highly variable genes from input sce... |
plotSeuratJackStraw | plotSeuratJackStraw Computes the plot object for jackstraw... |
plotSeuratReduction | plotSeuratReduction Plots the selected dimensionality... |
plotSoupXResults | Plot SoupX Result |
plotTopHVG | Plot highly variable genes |
plotTSCANClusterDEG | Plot features identified by 'runTSCANClusterDEAnalysis' on... |
plotTSCANClusterPseudo | Plot TSCAN pseudotime rooted from given cluster |
plotTSCANDimReduceFeatures | Plot feature expression on cell 2D embedding with MST... |
plotTSCANPseudotimeGenes | Plot expression changes of top features along a TSCAN... |
plotTSCANPseudotimeHeatmap | Plot heatmap of genes with expression change along TSCAN... |
plotTSCANResults | Plot MST pseudotime values on cell 2D embedding |
plotTSNE | Plot t-SNE plot on dimensionality reduction data run from... |
plotUMAP | Plot UMAP results either on already run results or run first... |
qcInputProcess | Create SingleCellExperiment object from command line input... |
readSingleCellMatrix | Read single cell expression matrix |
reportCellQC | Get runCellQC .html report |
reportClusterAbundance | Get plotClusterAbundance .html report |
reportDiffAbundanceFET | Get diffAbundanceFET .html report |
reportDiffExp | Get runDEAnalysis .html report |
reportDropletQC | Get runDropletQC .html report |
reportFindMarker | Get runFindMarker .html report |
reportQCTool | Get .html report of the output of the selected QC algorithm |
reportSeurat | Generates an HTML report for the complete Seurat workflow and... |
reportSeuratClustering | Generates an HTML report for Seurat Clustering and returns... |
reportSeuratDimRed | Generates an HTML report for Seurat Dimensionality Reduction... |
reportSeuratFeatureSelection | Generates an HTML report for Seurat Feature Selection and... |
reportSeuratMarkerSelection | Generates an HTML report for Seurat Results (including... |
reportSeuratNormalization | Generates an HTML report for Seurat Normalization and returns... |
reportSeuratResults | Generates an HTML report for Seurat Results (including... |
reportSeuratRun | Generates an HTML report for Seurat Run (including... |
reportSeuratScaling | Generates an HTML report for Seurat Scaling and returns the... |
retrieveSCEIndex | Retrieve cell/feature index by giving identifiers saved in... |
runBarcodeRankDrops | Identify empty droplets using barcodeRanks. |
runBBKNN | Apply BBKNN batch effect correction method to... |
runBcds | Find doublets/multiplets using bcds. |
runCellQC | Perform comprehensive single cell QC |
runClusterSummaryMetrics | Run Cluster Summary Metrics |
runComBatSeq | Apply ComBat-Seq batch effect correction method to... |
runCxds | Find doublets/multiplets using cxds. |
runCxdsBcdsHybrid | Find doublets/multiplets using cxds_bcds_hybrid. |
runDEAnalysis | Perform differential expression analysis on SCE object |
runDecontX | Detecting contamination with DecontX. |
runDimReduce | Generic Wrapper function for running dimensionality reduction |
runDoubletFinder | Generates a doublet score for each cell via doubletFinder |
runDropletQC | Perform comprehensive droplet QC |
runEmptyDrops | Identify empty droplets using emptyDrops. |
runEnrichR | Run EnrichR on SCE object |
runFastMNN | Apply a fast version of the mutual nearest neighbors (MNN)... |
runFeatureSelection | Run Variable Feature Detection Methods |
runFindMarker | Find the marker gene set for each cluster |
runGSVA | Run GSVA analysis on a SingleCellExperiment object |
runHarmony | Apply Harmony batch effect correction method to... |
runKMeans | Get clustering with KMeans |
runLimmaBC | Apply Limma's batch effect correction method to... |
runMNNCorrect | Apply the mutual nearest neighbors (MNN) batch effect... |
runModelGeneVar | Calculate Variable Genes with Scran modelGeneVar |
runNormalization | Run normalization/transformation with various methods |
runPerCellQC | Wrapper for calculating QC metrics with scater. |
runSCANORAMA | Apply the mutual nearest neighbors (MNN) batch effect... |
runScanpyFindClusters | runScanpyFindClusters Computes the clusters from the input... |
runScanpyFindHVG | runScanpyFindHVG Find highly variable genes and store in the... |
runScanpyFindMarkers | runScanpyFindMarkers |
runScanpyNormalizeData | runScanpyNormalizeData Wrapper for NormalizeData() function... |
runScanpyPCA | runScanpyPCA Computes PCA on the input sce object and stores... |
runScanpyScaleData | runScanpyScaleData Scales the input sce object according to... |
runScanpyTSNE | runScanpyTSNE Computes tSNE from the given sce object and... |
runScanpyUMAP | runScanpyUMAP Computes UMAP from the given sce object and... |
runScDblFinder | Detect doublet cells using scDblFinder. |
runSCMerge | Apply scMerge batch effect correction method to... |
runScranSNN | Get clustering with SNN graph |
runScrublet | Find doublets using 'scrublet'. |
runSeuratFindClusters | runSeuratFindClusters Computes the clusters from the input... |
runSeuratFindHVG | runSeuratFindHVG Find highly variable genes and store in the... |
runSeuratFindMarkers | runSeuratFindMarkers |
runSeuratHeatmap | runSeuratHeatmap Computes the heatmap plot object from the... |
runSeuratICA | runSeuratICA Computes ICA on the input sce object and stores... |
runSeuratIntegration | runSeuratIntegration A wrapper function to Seurat... |
runSeuratJackStraw | runSeuratJackStraw Compute jackstraw plot and store the... |
runSeuratNormalizeData | runSeuratNormalizeData Wrapper for NormalizeData() function... |
runSeuratPCA | runSeuratPCA Computes PCA on the input sce object and stores... |
runSeuratScaleData | runSeuratScaleData Scales the input sce object according to... |
runSeuratSCTransform | runSeuratSCTransform Runs the SCTransform function to... |
runSeuratTSNE | runSeuratTSNE Computes tSNE from the given sce object and... |
runSeuratUMAP | runSeuratUMAP Computes UMAP from the given sce object and... |
runSingleR | Label cell types with SingleR |
runSoupX | Detecting and correct contamination with SoupX |
runTSCAN | Run TSCAN to obtain pseudotime values for cells |
runTSCANClusterDEAnalysis | Find DE genes between all TSCAN paths rooted from given... |
runTSCANDEG | Test gene expression changes along a TSCAN trajectory path |
runTSNE | Run t-SNE embedding with Rtsne method |
runUMAP | Run UMAP embedding with scater method |
runVAM | Run VAM to score gene sets in single cell data |
runZINBWaVE | Apply ZINBWaVE Batch effect correction method to... |
sampleSummaryStats | Generate table of SCTK QC outputs. |
scaterCPM | scaterCPM Uses CPM from scater library to compute... |
scaterlogNormCounts | scaterlogNormCounts Uses logNormCounts to log normalize input... |
scaterPCA | Perform scater PCA on a SingleCellExperiment Object |
sce | Example Single Cell RNA-Seq data in SingleCellExperiment... |
sceBatches | Example Single Cell RNA-Seq data in SingleCellExperiment... |
sctkListGeneSetCollections | Lists imported GeneSetCollections |
sctkPythonInstallConda | Installs Python packages into a Conda environment |
sctkPythonInstallVirtualEnv | Installs Python packages into a virtual environment |
SEG | Stably Expressed Gene (SEG) list obect, with SEG sets for... |
selectSCTKConda | Selects a Conda environment |
selectSCTKVirtualEnvironment | Selects a virtual environment |
setRowNames | Set rownames of SCE with a character vector or a rowData... |
setSCTKDisplayRow | Indicates which rowData to use for visualization |
singleCellTK | Run the single cell analysis app |
subDiffEx | Passes the output of generateSimulatedData() to differential... |
subsetSCECols | Subset a SingleCellExperiment object by columns |
subsetSCERows | Subset a SingleCellExperiment object by rows |
summarizeSCE | Summarize an assay in a SingleCellExperiment |
trimCounts | Trim Counts |
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