Man pages for JEFworks/MUDAN
Multi-sample Unified Discriminant ANalysis
| cleanCounts | Filter a counts matrix |
| clusterBasedBatchCorrect | Batch correct within identified groups using ComBat |
| fastPca | Derive principal components by SVD |
| getApproxComMembership | Get clusters by community detection on approximate nearest... |
| getComMembership | Get clusters by community detection on approximate nearest... |
| getConfidentPreds | Use LDA model posteriors to retain only confident predictions |
| getDifferentialGenes | Differential expression analysis (adapted from PAGODA2) |
| getPcs | Dimensionality reduction by PCA |
| getStableClusters | Iterative merging of clusters along tree until stable |
| getVariableGenes | Get variable genes |
| mergePredsList | Merge a list of group annotations |
| modelLda | Linear discriminant analysis model |
| Mudan | R6 object for storing all relevant output from MUDAN analysis... |
| normalizeCounts | Normalizes counts to CPM |
| normalizeVariance | Normalize gene expression variance relative to... |
| pbmcA | Frozen PBMCs (Donor A) |
| pbmcB | Frozen PBMCs (Donor B) |
| pbmcC | Frozen PBMCs (Donor C) |
| plotEmbedding | Plot 2D embedding |
| predictLds | Predict LD embedding for new dataset given old model and gene... |
| referenceAnnot | Annotations for sorted CD14+ Monocytes CD19+ B Cells, CD34+... |
| referenceCounts | Sorted CD14+ Monocytes CD19+ B Cells, CD34+ Cells, CD4+... |
| tsneLda | Run tSNE on LDs from model |
