Interactive Analysis of Single Cell RNA-Seq Data


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Documentation for package ‘singleCellTK’ version 1.2.3

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alignSingleCellData Align Single Cell RNA-Seq Data and Create a SCtkExperiment Object
calcEffectSizes Finds the effect sizes for all genes in the original dataset, regardless of significance.
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 differentially expressed genes, and median significant effect size
DownsampleDepth Estimate numbers of detected genes, significantly differentially expressed genes, and median significant effect size
enrichRSCE enrichR Given a list of genes this function runs the enrichR() to perform Gene enrichment
filterSCData Filter Genes and Samples from a Single Cell Object
generateSimulatedData Generates a single simulated dataset, bootstrapping from the input counts matrix.
getBiomarker Get and plot PCA and t-SCE components for a SCtkE object
getClusterInputData Get data to use as input clustering algorithms
getPCA Get and plot PCA and t-SCE components for a SCtkE object
getTSNE Get and plot PCA and t-SCE components for a SCtkE object
gsvaPlot gsvaSCE
gsvaSCE gsvaSCE
iterateSimulations Returns significance data from a snapshot.
MAST MAST
MASTregression MAST
MASTviolin MAST
mouseBrainSubsetSCE Example Single Cell RNA-Seq data in SCtkExperiment Object, GSE60361 subset
parseRsubreadLogs Parse Rsubread Logs for Mapping and Feature Count Statistics
pcaVariances Get PCA variances
pcaVariances-method Get PCA variances
pcaVariances<- Set PCA variances
pcaVariances<--method Get PCA variances
plotBatchVariance Plot the percent of the variation that is explained by batch and condition in the data
plotBiomarker Get and plot PCA and t-SCE components for a SCtkE object
plotDiffEx Plot Differential Expression
plotPCA Get and plot PCA and t-SCE components for a SCtkE object
plotTSNE Get and plot PCA and t-SCE components for a SCtkE object
saveBiomarkerRes saveBiomarkerRes Save biomarker gene information with a custom name when provided with diffex results.
saveDiffExResults saveDiffExResults Save Differential Expression Results with a custom name.
scDiffEx Perform differential expression analysis on a SCtkExperiment object
scDiffExANOVA Perform differential expression analysis on a SCtkExperiment object
scDiffExDESeq2 Perform differential expression analysis on a SCtkExperiment object
scDiffExlimma Perform differential expression analysis on a SCtkExperiment object
SCtkExperiment Create a SCtkExperiment
SCtkExperiment-class A lightweight S4 extension to the SingleCellExperiment class to store additional information.
singleCellTK Run the single cell analysis app
subDiffEx Passes the output of generateSimulatedData() to differential expression tests, picking either t-tests or ANOVA for data with only two conditions or multiple conditions, respectively.
subDiffExANOVA Passes the output of generateSimulatedData() to differential expression tests, picking either t-tests or ANOVA for data with only two conditions or multiple conditions, respectively.
subDiffExttest Passes the output of generateSimulatedData() to differential expression tests, picking either t-tests or ANOVA for data with only two conditions or multiple conditions, respectively.
summarizeTable Summarize SCtkExperiment
thresholdGenes MAST
visPlot visPlot