Man pages for 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... |
| computeZScore | Compute Z-Score |
| constructSCE | Create SingleCellExperiment object from csv or txt input |
| convertGeneIDs | Convert Gene IDs |
| convertSCEToSeurat | convertSCEToSeurat Converts sce object to seurat while... |
| convertSeuratToSCE | convertSeuratToSCE Converts the input seurat object to a sce... |
| dataAnnotationColor | Generate distinct colors for all categorical col/rowData... |
| discreteColorPalette | Generate given number of color codes |
| distinctColors | Generate a distinct palette for coloring different clusters |
| dot-addSeuratToMetaDataSCE | .addSeuratToMetaDataSCE Adds the input seurat object to the... |
| dot-checkDiffExpResultExists | Check if the specified MAST result in SingleCellExperiment... |
| dot-computeSignificantPC | .computeSignificantPC Computes the significant principal... |
| dot-extractSCEAnnotation | Extract columns from row/colData and transfer to factors |
| dot-formatDEAList | Helper function for differential expression analysis methods... |
| dot-getComponentNames | .getComponentNames Creates a list of PC/IC components to... |
| dot-ggBar | Bar plot plotting tool. |
| dot-ggDensity | Density plot plotting tool. |
| dot-ggScatter | Plot results of reduced dimensions data. |
| dot-ggViolin | Violin plot plotting tool. |
| dot-sce2adata | Coverts SingleCellExperiment object from R to anndata.AnnData... |
| dot-seuratGetVariableFeatures | .seuratGetVariableFeatures Retrieves the requested number of... |
| dot-seuratInvalidate | .seuratInvalidate Removes seurat data from the input... |
| dot-updateAssaySCE | .updateAssaySCE Update/Modify/Add an assay in the provided... |
| downSampleCells | Estimate numbers of detected genes, significantly... |
| downSampleDepth | Estimate numbers of detected genes, significantly... |
| enrichRSCE | enrichR Given a list of genes this function runs 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 |
| featureIndex | Retrieve row index for a set of features |
| findMarkerDiffExp | Find the marker gene set for each cluster With an input... |
| generateMeta | Generate 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,... |
| getMSigDBTable | Shows MSigDB categories |
| getPCA | Perform PCA on a SingleCellExperiment Object A wrapper to... |
| getSceParams | Extract QC parameters from the SingleCellExperiment object |
| getTopHVG | getTopHVG Extracts the top variable genes from an input... |
| getTSNE | Run t-SNE dimensionality reduction method on a... |
| getUMAP | Uniform Manifold Approximation and Projection(UMAP) algorithm... |
| gsvaSCE | Run GSVA analysis on a SingleCellExperiment object |
| 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 |
| 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. |
| mergeSCEColData | Merging colData from two singleCellExperiment objects |
| mouseBrainSubsetSCE | Example Single Cell RNA-Seq data in SingleCellExperiment... |
| msigdb_table | MSigDB gene get Cctegory table |
| plotBarcodeRankDropsResults | Plots for runEmptyDrops outputs. |
| plotBarcodeRankScatter | Plots for runBarcodeRankDrops outputs. |
| plotBatchVariance | Plot the percent of the variation that is explained by batch... |
| plotBcdsResults | Plots for runBcds outputs. |
| plotBiomarker | Given a set of genes, return a ggplot of expression values. |
| plotCxdsResults | Plots for runCxds outputs. |
| plotDecontXResults | Plots for runDecontX outputs. |
| plotDEGHeatmap | Heatmap visualization of DEG result |
| plotDEGRegression | plot the linear regression to show visualize the expression... |
| plotDEGViolin | plot the violin plot to show visualize the expression... |
| plotDoubletCellsResults | Plots for runDoubletCells outputs. |
| plotDoubletFinderResults | Plots for runDoubletFinder outputs. |
| plotEmptyDropsResults | Plots for runEmptyDrops outputs. |
| plotEmptyDropsScatter | Plots for runEmptyDrops outputs. |
| plotMarkerDiffExp | Plot a heatmap to visualize the result of 'findMarkerDiffExp' |
| plotMASTThresholdGenes | MAST Identify adaptive thresholds |
| plotPCA | Plot PCA run data from its components. |
| plotRunPerCellQCResults | Plots for runPerCellQC 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. |
| 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 |
| reportDiffExp | Get runDEAnalysis .html report |
| reportDropletQC | Get runDropletQC .html report |
| reportQCTool | Get .html report of the output of the selected QC algorithm |
| retrieveSCEIndex | Retrieve cell/feature index by giving identifiers saved in... |
| runANOVA | Perform differential expression analysis on SCE with ANOVA |
| 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 |
| runComBat | Apply ComBat 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 with... |
| runDecontX | Detecting contamination with DecontX. |
| runDESeq2 | Perform differential expression analysis on SCE with DESeq2. |
| runDoubletCells | Detect doublet cells using scDblFinder. |
| runDoubletFinder | Generates a doublet score for each cell via doubletFinder |
| runDropletQC | Perform comprehensive droplet QC |
| runEmptyDrops | Identify empty droplets using emptyDrops. |
| runFastMNN | Apply a fast version of the mutual nearest neighbors (MNN)... |
| runKMeans | Get clustering with KMeans |
| runLimmaBC | Apply Limma's batch effect correction method to... |
| runLimmaDE | Perform differential expression analysis on SCE with Limma. |
| runMAST | Perform differential expression analysis on SCE with MAST |
| runMNNCorrect | Apply the mutual nearest neighbors (MNN) batch effect... |
| runPerCellQC | Wrapper for calculating QC metrics with scater. |
| runSCANORAMA | Apply the mutual nearest neighbors (MNN) batch effect... |
| runSCMerge | Apply scMerge batch effect correction method to... |
| runScranSNN | Get clustering with SNN graph |
| runScrublet | Find doublets using 'scrublet'. |
| runZINBWaVE | Apply ZINBWaVE Batch effect correction method to... |
| sampleSummaryStats | Generate table of SCTK QC outputs. |
| scater_logNormCounts | scater_logNormCounts Uses logNormCounts to log normalize... |
| sce | Example Single Cell RNA-Seq data in SingleCellExperiment... |
| sceBatches | Example Single Cell RNA-Seq data in SingleCellExperiment... |
| scran_modelGeneVar | scran_modelGeneVar Generates and stores variability data from... |
| 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 |
| seuratComputeHeatmap | seuratComputeHeatmap Computes the heatmap plot object from... |
| seuratComputeJackStraw | seuratComputeJackStraw Compute jackstraw plot and store the... |
| seuratElbowPlot | seuratElbowPlot Computes the plot object for elbow plot from... |
| seuratFindClusters | seuratFindClusters Computes the clusters from the input sce... |
| seuratFindHVG | seuratFindHVG Find highly variable genes and store in the... |
| seuratHeatmapPlot | seuratHeatmapPlot Modifies the heatmap plot object so it... |
| seuratICA | seuratICA Computes ICA on the input sce object and stores the... |
| seuratIntegration | seuratIntegration A wrapper function to Seurat... |
| seuratJackStrawPlot | seuratJackStrawPlot Computes the plot object for jackstraw... |
| seuratNormalizeData | seuratNormalizeData Wrapper for NormalizeData() function from... |
| seuratPCA | seuratPCA Computes PCA on the input sce object and stores the... |
| seuratPlotHVG | seuratPlotHVG Plot highly variable genes from input sce... |
| seuratReductionPlot | seuratReductionPlot Plots the selected dimensionality... |
| seuratRunTSNE | seuratRunTSNE Computes tSNE from the given sce object and... |
| seuratRunUMAP | seuratRunUMAP Computes UMAP from the given sce object and... |
| seuratScaleData | seuratScaleData Scales the input sce object according to the... |
| seuratSCTransform | seuratSCTransform Runs the SCTransform function to... |
| simpleLog | A decorator that prints the arguments to the decorated... |
| 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 |
| visPlot | visPlot |
