Man pages for mmkhan19/singleCellTK
Interactive Analysis of Single Cell RNA-Seq Data
| alignSingleCellData | Align Single Cell RNA-Seq Data and Create a SCtkExperiment... |
| calcEffectSizes | Finds the effect sizes for all genes in the original dataset,... |
| campbellBrainSubset | Example Single Cell RNA-Seq data in SCtkExperiment Object,... |
| ComBatSCE | ComBatSCE |
| convertGeneIDs | Convert Gene IDs |
| createSCE | Create a SCtkExperiment object |
| distinctColors | Generate a distinct palette for coloring different clusters |
| 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... |
| filterSCData | Filter Genes and Samples from a Single Cell Object |
| generateSimulatedData | Generates a single simulated dataset, bootstrapping from the... |
| getBiomarker | Given a list of genes and a SCtkExperiment object, return the... |
| getClusterInputData | Get data to use as input clustering algorithms |
| getPCA | Get and plot PCA components for a SCtkE object |
| getTSNE | Run t-SNE dimensionality reduction method on the assay data. |
| getUMAP | Uniform Manifold Approximation and Projection(UMAP) algorithm... |
| gsvaSCE | Run GSVA analysis on a SCtkExperiment object. |
| iterateSimulations | Returns significance data from a snapshot. |
| MAST | MAST |
| mouseBrainSubsetSCE | Example Single Cell RNA-Seq data in SCtkExperiment Object,... |
| parseRsubreadLogs | Parse Rsubread Logs for Mapping and Feature Count Statistics |
| pcaVariances | Get PCA variances |
| pcaVariances-set | Set PCA variances |
| plotBatchVariance | Plot the percent of the variation that is explained by batch... |
| plotBiomarker | Given a set of genes, return a ggplot of expression values. |
| plotDiffEx | Plot Differential Expression |
| plotDimRed | Plot results either on already run results of reduced... |
| plotPCA | Plot PCA run data from its components. |
| plotTSNE | Plot t-SNE plot on dimensionality reduction data run from... |
| plotUMAP | Plot UMAP results either on already run results or run first... |
| saveBiomarkerRes | saveBiomarkerRes Save biomarker gene information with a... |
| saveDiffExResults | saveDiffExResults Save Differential Expression Results with a... |
| scDiffEx | Perform differential expression analysis on a SCtkExperiment... |
| SCtkExperiment | Create a SCtkExperiment |
| SCtkExperiment-class | A lightweight S4 extension to the SingleCellExperiment class... |
| singleCellTK | Run the single cell analysis app |
| subDiffEx | Passes the output of generateSimulatedData() to differential... |
| summarizeTable | Summarize SCtkExperiment |
| visPlot | visPlot |
