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 |