Man pages for dviraran/SingleR
Reference-based single-cell RNA-seq annotation
| blueprint_encode | Blueprint+Encode reference dataset for human |
| calculateSignatures | Calculate single-sample gene set enrichment (ssGSEA) for each... |
| cell.type.classification | Reference matrix for Kang et al. classification |
| clusters.map.values | Map clusters to values |
| Combine.Multiple.10X.Datasets | Helper function to combine multiple 10X datasets |
| convertSingleR2Browser | Convert the SingleR output object to a SingleR S4 object that... |
| CreateBigSingleRObject | Analyze very big data sets. Runs SingleR on small chunks... |
| CreateSinglerObject | Wrapper function to create a SingleR object |
| CreateSinglerSeuratObject | Wrapper function to create a SingleR object + Seurat object |
| CreateVariableGeneSet | Create a list for differential genes for all pairwise cell... |
| fineTuningRound | Internal function for a step in the fine-tuning process |
| hpca | Human Primary Cell Atlas (HPCA) reference dataset for human |
| human.egc | Human signatures |
| human_lengths | Length of human genes for TPM calculation |
| immgen | Immgen reference dataset for mouse |
| medianMatrix | Calculate median values by groups |
| mouse.egc | Mouse signatures |
| mouse_lengths | Length of mouse genes for TPM calculation |
| mouse.rnaseq | Mouse-RNAseq reference dataset for mouse |
| quantileMatrix | Calculate a quantile value by groups |
| ReadSingleCellData | Internal function to read single-cell data |
| remove.Unnecessary.Data.single | Remove data from a SingleR object to make it smaller |
| SingleR | The main SingleR function |
| SingleR-class | An S4 class to represent SingleR objects This object can be... |
| SingleR.Cluster | SingleR.Cluster - using the scores data to cluster single... |
| SingleR.Combine | Combining SingleR objects together to one object. |
| SingleR.ConfidenceTest | Test confidence of SingleR annotation. |
| SingleR.CreateKangAnnotations | Run annotation based on Kang et al. Nature Biotechnology... |
| SingleR.CreateObject | Wrapper function to create a SingleR object |
| SingleR.CreateSeurat | Wrapper function to create a Seurat object |
| SingleR.DrawBoxPlot | Plot boxplots for each label for a given single cell. |
| SingleR.DrawHeatmap | Plot a heatmap of the scores for all the single cells |
| SingleR.DrawScatter | Plot a scatter plot of a single cell vs. a reference sample |
| SingleR.FineTune | SingleR fine-tuning function. Takes top scores per cell type,... |
| SingleR.PlotFeature | Plot a feature on the t-SNE plot |
| SingleR.PlotTsne | Plot a colored tSNE plot according to a set of labels |
| SingleR.ScoreData | Scoring single cells using reference data set |
| SingleR.Subset | Subseting a SingleR object. This function subsets all the... |
| superRef | Creating a subset of the super reference dataset |
| TPM | Normalize counts to gene length |
