| aggregateGeneSetScores | Take difference of two paired bi-directional gene set scores |
| cKmeansDownsampleSmallest | Wrapper for constrained K-means on data subsampled to the... |
| cKmeansDownsampleSqrt | Wrapper for constrained K-means on data subsampled to the... |
| getDGEInter | Create interactive table of differential gene expression... |
| getDGETable | Extract table of differential results from 'K2' object |
| getEnrichmentInter | Create interactive table of gene set enrichment results from... |
| getEnrichmentTable | Extract table of enrichment results from 'K2' object |
| getGenePathways | Map features (genes) to feature list (genesets) |
| hclustWrapper | Wrapper for hierarchical clustering |
| K2colData | Data frame of phenotypic information from K2 object |
| K2dashboard | Generate interactive dashboard of K2 Taxonomer results |
| K2data | Data matrix from K2 object |
| K2dendro | Reformat K2Taxonomer results to dendrogram object |
| K2eMat | Expression matrix object used in partitioning |
| K2eMatDS | Expression matrix object used for differential expression |
| K2gene2Pathway | Vector of collapsed pathways for which each gene belongs |
| K2genesets | Named list of genesets used in K2Taxonomer run |
| K2genesetURL | Assign URLs to genesets included in K2Taxonomer run |
| K2geneURL | Assign URLs to genes included in K2Taxonomer run |
| K2gMat | Numeric matrix of enrichment scores |
| K2meta | Meta data defining parameters of K2Taxonomer run |
| K2preproc | Function to create K2 object for pre-processing |
| K2res | Example K2Taxonomer output |
| K2results | Annotated list of partition assignments from K2Taxonomer run |
| K2tax | Function to K2 Taxonomer partitioning |
| K2visNetwork | Interactive K2 dendrogram |
| matrixORdgCMatrix-class | K2 object |
| plotGenePathway | Plot gene expression or enrichment scores |
| runDGEmods | Perform differential analysis between subgroups at each... |
| runDSSEmods | Perform differential analysis of enrichment scores between... |
| runFISHERmods | Perform Fisher test overrepresentation analysis of each... |
| runScoreGeneSets | Enrichment scoring of gene sets on expression data |
