Man pages for singleCellTK
Interactive Analysis of Single Cell RNA-Seq Data

alignSingleCellDataAlign Single Cell RNA-Seq Data and Create a SCtkExperiment...
calcEffectSizesFinds the effect sizes for all genes in the original dataset,...
ComBatSCEComBatSCE
convertGeneIDsConvert Gene IDs
createSCECreate a SCtkExperiment object
distinctColorsGenerate a distinct palette for coloring different clusters
DownsampleCellsEstimate numbers of detected genes, significantly...
DownsampleDepthEstimate numbers of detected genes, significantly...
enrichRSCEenrichR Given a list of genes this function runs the...
filterSCDataFilter Genes and Samples from a Single Cell Object
generateSimulatedDataGenerates a single simulated dataset, bootstrapping from the...
getBiomarkerGiven a list of genes and a SCtkExperiment object, return the...
getClusterInputDataGet data to use as input clustering algorithms
getPCAGet and plot PCA components for a SCtkE object
getTSNERun t-SNE dimensionality reduction method on the assay data.
getUMAPUniform Manifold Approximation and Projection(UMAP) algorithm...
gsvaSCERun GSVA analysis on a SCtkExperiment object.
iterateSimulationsReturns significance data from a snapshot.
MASTMAST
mouseBrainSubsetSCEExample Single Cell RNA-Seq data in SCtkExperiment Object,...
parseRsubreadLogsParse Rsubread Logs for Mapping and Feature Count Statistics
pcaVariancesGet PCA variances
pcaVariances-setSet PCA variances
plotBatchVariancePlot the percent of the variation that is explained by batch...
plotBiomarkerGiven a set of genes, return a ggplot of expression values.
plotDiffExPlot Differential Expression
plotDimRedPlot results either on already run results of reduced...
plotPCAPlot PCA run data from its components.
plotTSNEPlot t-SNE plot on dimensionality reduction data run from...
plotUMAPPlot UMAP results either on already run results or run first...
saveBiomarkerRessaveBiomarkerRes Save biomarker gene information with a...
saveDiffExResultssaveDiffExResults Save Differential Expression Results with a...
scDiffExPerform differential expression analysis on a SCtkExperiment...
SCtkExperimentCreate a SCtkExperiment
SCtkExperiment-classA lightweight S4 extension to the SingleCellExperiment class...
singleCellTKRun the single cell analysis app
subDiffExPasses the output of generateSimulatedData() to differential...
summarizeTableSummarize SCtkExperiment
visPlotvisPlot
singleCellTK documentation built on Oct. 31, 2019, 5:59 a.m.