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| diffcyt-package | Run 'diffcyt' pipeline |
| calcCounts | Calculate cluster cell counts |
| calcMedians | Calculate cluster medians |
| calcMediansByClusterMarker | Calculate medians (by cluster and marker) |
| calcMediansBySampleMarker | Calculate medians (by sample and marker) |
| createContrast | Create contrast matrix |
| createDesignMatrix | Create design matrix |
| createFormula | Create model formula and corresponding data frame of variables |
| diffcyt | Run 'diffcyt' pipeline |
| generateClusters | Generate clusters |
| plotHeatmap | Plot heatmap |
| prepareData | Prepare data |
| testDA_edgeR | Test for differential abundance: method 'diffcyt-DA-edgeR' |
| testDA_GLMM | Test for differential abundance: method 'diffcyt-DA-GLMM' |
| testDA_voom | Test for differential abundance: method 'diffcyt-DA-voom' |
| testDS_limma | Test for differential states: method 'diffcyt-DS-limma' |
| testDS_LMM | Test for differential states: method 'diffcyt-DS-LMM' |
| topClusters | Alias for 'topTable' (deprecated) |
| topTable | Show table of results for top clusters or cluster-marker combinations |
| transformData | Transform data |