Man pages for data2intelligence/SpaCE
Spatial Cellular Estimator for Tumors
| addTo.Seurat | Add SpaCET to Seurat |
| convert.Seurat | Convert Seurat to SpaCET |
| create.SpaCET.object | Create an SpaCET object |
| create.SpaCET.object.10X | Create an SpaCET object from 10X Visium |
| read.gmt | Read a gmt file. |
| SpaCET.CCI.cellTypePair | Ligand-Receptor analysis for a co-localized cell-type pair |
| SpaCET.CCI.colocalization | Cell-cell colocalization analysis |
| SpaCET.CCI.LRNetworkScore | Ligand-Receptor interaction enrichment analysis |
| SpaCET-class | Define the SpaCET object |
| SpaCET.combine.interface | Combine interaction spots to interface |
| SpaCET.deconvolution | Deconvolve tumor ST data set |
| SpaCET.deconvolution.malignant | Deconvolve malignant cell fraction |
| SpaCET.deconvolution.matched.scRNAseq | Deconvolve ST data set with matched scRNAseq data |
| SpaCET.distance.to.interface | Distance to tumor border |
| SpaCET.GeneSetScore | Calculate gene set score for each spot. |
| SpaCET.identify.interface | Identify tumor-stroma interface |
| SpaCET.quality.control | Filter spatial spots and calculate the QC metrics |
| SpaCET.visualize.cellTypePair | Cell-type pair visualization |
| SpaCET.visualize.colocalization | Cell-cell colocalization visualization |
| SpaCET.visualize.spatialFeature | Spatial feature visualization |
| write.gmt | Write a gmt file. |
