Man pages for lingxuez/SOUP
Semi-soft Clustering of Single Cell Data
| camp | The fetal brain single-cell dataset. |
| cv.error.SOUP | Compute cross validation errors |
| cvSOUP | Cross validation for SOUP |
| deconvG | Base function of G-modeling deconvolution |
| deconvSingle | Deconvolve the true gene expression distribution of a single... |
| DESCEND | An S4 class object containing the DESCEND result for a single... |
| DESCEND.control | The control parameters of the function 'runDescend' and... |
| DESCENDselect | DESCEND gene selection |
| findHVG | Finding highly variable genes (HVG) based on Gini... |
| findPure | Find pure cells |
| getCenters | Get cluster centers |
| getClusterLineages | Get lineages from cluster centers |
| getClusterOrder | Order clusters |
| getDescendants | Get descendants in a tree |
| getEstimates | Grab the value and standard deviation of the estimated... |
| getLineageCurves | Get lineage curves |
| getLineageTime | Decide cell pseudotime |
| getMajorMatrix | Get the SOUP hard assignment matrix |
| getPermute | Permute labels |
| getPval | Grab the likelihood ratio test p-values if the tests are... |
| getSimilarity | Compute similarity matrix |
| getTheta | Get the membership matrix and centers |
| getTimeline | Estimate developmental trajectory |
| heatmapKseq | Visualize SOUP hard assignments. |
| plotContTable | Visualize contingency table |
| plotGeneTimeline | Plot gene expression along trajectory |
| plotLineageCurves | Plot lineages or curves |
| plotMultipleGeneTimeline | Plot multiple gene expressions along trajectory |
| predictTheta | Predict the membership for new data points |
| projMembership | Clean up membership matrix |
| runDescend | Apply DESCEND to all the genes in the count matrix for one... |
| scaleRowSums | Scale matrix by row sums |
| selectGenes | Select highly variable genes |
| SOUP | SOUP |
| SPCAselect | SPCA gene selection |
| zeisel | The mouse brain single-cell dataset |
