Man pages for compbiomed/singleCellTK
Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data
| 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 |
