Man pages for carmonalab/ProjecTILs
Reference-based analysis of scRNA-seq data
| cellstate.predict | Predict cell states of a projected dataset |
| celltype.heatmap | Plot a averaged expression heatmap from a Seurat object |
| compute_silhouette | Calculate Silhouette coefficient |
| FindAllMarkers.bygroup | Gene expression markers shared by multiple groups of cells |
| find.discriminant.dimensions | Find discriminant dimensions |
| find.discriminant.genes | Find discriminant genes |
| get.reference.maps | Retrieve and load reference atlas |
| list.reference.maps | Available reference atlas for ProjecTILs |
| load.reference.map | Load Reference Atlas |
| make.projection | Project a query scRNA-seq dataset onto a reference atlas |
| make.reference | Make a ProjecTILs reference |
| merge.Seurat.embeddings | Merge Seurat objects, including reductions (e.g. PCA, UMAP,... |
| plot.discriminant.3d | 3D plot of reference map with extra discriminant dimension |
| plot.projection | Show UMAP projection of query on reference map |
| plot.statepred.composition | Summarize the predicted cell states of an object |
| plot.states.radar | Show expression level of key genes |
| ProjecTILs.classifier | Annotate query dataset using a reference object |
| read.sc.query | Read to memory a query expression matrix |
| recalculate.embeddings | Recalculate low dimensional embeddings after projection |
| Run.ProjecTILs | Project a query scRNA-seq dataset onto a reference atlas |
