Man pages for dviraran/SingleR
Reference-based single-cell RNA-seq annotation

blueprint_encodeBlueprint+Encode reference dataset for human
calculateSignaturesCalculate single-sample gene set enrichment (ssGSEA) for each...
cell.type.classificationReference matrix for Kang et al. classification
clusters.map.valuesMap clusters to values
Combine.Multiple.10X.DatasetsHelper function to combine multiple 10X datasets
CreateSinglerObjectWrapper function to create a SingleR object
CreateSinglerSeuratObjectWrapper function to create a SingleR object + Seurat object
CreateVariableGeneSetCreate a list for differential genes for all pairwise cell...
fineTuningRoundInternal function for a step in the fine-tuning process
hpcaHuman Primary Cell Atlas (HPCA) reference dataset for human
human.egcHuman signatures
human_lengthsLength of human genes for TPM calculation
immgenImmgen reference dataset for mouse
medianMatrixCalculate median values by groups
mouse.egcMouse signatures
mouse_lengthsLength of mouse genes for TPM calculation
mouse.rnaseqMouse-RNAseq reference dataset for mouse
quantileMatrixCalculate a quantile value by groups
ReadSingleCellDataInternal function to read single-cell data
remove.Unnecessary.Data.singleRemove data from a SingleR object to make it smaller
SingleRThe main SingleR function
SingleR.ClusterSingleR.Cluster - using the scores data to cluster single...
SingleR.CombineCombining SingleR objects together to one object.
SingleR.ConfidenceTestTest confidence of SingleR annotation.
SingleR.CreateKangAnnotationsRun annotation based on Kang et al. Nature Biotechnology...
SingleR.CreateObjectWrapper function to create a SingleR object
SingleR.CreateSeuratWrapper function to create a Seurat object
SingleR.DrawBoxPlotPlot boxplots for each label for a given single cell.
SingleR.DrawHeatmapPlot a heatmap of the scores for all the single cells
SingleR.DrawScatterPlot a scatter plot of a single cell vs. a reference sample
SingleR.FineTuneSingleR fine-tuning function. Takes top scores per cell type,...
SingleR.PlotFeaturePlot a feature on the t-SNE plot
SingleR.PlotTsnePlot a colored tSNE plot according to a set of labels
SingleR.ScoreDataScoring single cells using reference data set
SingleR.SubsetSubseting a SingleR object. This function subsets all the...
superRefCreating a subset of the super reference dataset
TPMNormalize counts to gene length
dviraran/SingleR documentation built on Nov. 9, 2018, 12:23 p.m.