Man pages for BodenmillerGroup/imcRtools
Methods for imaging mass cytometry data analysis
| aggregateNeighbors | Function to aggregate all neighbors of each cell. |
| binAcrossPixels | Aggregate consecutive pixels per single-metal spot |
| buildSpatialGraph | Builds an interaction graph based on the cells' locations |
| countInteractions | Summarizes cell-cell interactions within grouping levels... |
| detectCommunity | Detect the spatial community of each cell |
| detectSpatialContext | Detect the spatial context of each cell based on its... |
| filterPixels | Filter pixels based on their assigned masses |
| filterSpatialContext | Filter spatial contexts |
| findBorderCells | Find cells at the image border |
| minDistToCells | Function to calculate minimal distance to cells of interest |
| patchDetection | Function to detect patches containing defined cell types |
| patchSize | Function to compute the area of c3ll patches |
| plotSpatial | Visualizes the spatial locations and interactions of cells |
| plotSpatialContext | Plot spatial context graph |
| plotSpotHeatmap | Summarizes and visualizes the pixel intensities per spot and... |
| read_cpout | Reads in single-cell data generated by the... |
| readImagefromTXT | Reads one or multiple .txt files into a CytoImageList object |
| readSCEfromTXT | Generates a SingleCellExperiment from .txt files |
| read_steinbock | Reads in single-cell data generated by the steinbock pipeline |
| show_cpout_features | Display all features measured by CellProfiler. |
| testInteractions | Tests if cell types interact more or less frequently than... |
