Man pages for uc-bd2k/CLEAN
Clustering Enrichment Analysis
| annotateChipSeqPeaks | Function to match each peaks to associated genes in terms of... |
| bCa | Sets of p-values derived from two breast cancer data sets. |
| call.treeview | Function to call the standalone fTreeView Java application |
| cdt2r | Functions to import files in TreeView format into R. |
| chipSeqWeightedSum | Calculate binding strengh by summing weighted chip-seq peaks. |
| CLEAN-package | Clustering Enrichment Analysis |
| cMap | A set of p-values derived from the Connectivity Map dataset. |
| convertFunctionalCategories | Function to convert Entrez gene ID-based functional... |
| createRefGenome | Function to match download ref genome platform from UCSC. |
| enrichmentGSEA | Performing GSEA analysis with the fgsea package |
| generateTreeViewFiles | Wrapper function to perform functional Clustering Enrichment... |
| geneSigInClustering | Auxiliary functions to funcClustAnnot and geneListEnrichment |
| genesInEnrichedCategories | Function to intersect a gene list with enriched categories |
| getBinarySubTree | Get the left or right subtree of a given hierarchical... |
| getFuntionalCategories | Retrieve functional categories from species-specific library. |
| gimmOut | An gimmR object, i.e. a list containing a dataframe with gene... |
| GRS | Function to calculate the Generalized Random Set statistic to... |
| LRpath | Testing GO terms or KEGG with logistic regression |
| nonHierarchicalClustering | Convert a non-hierarchical clustering into hierarchical... |
| plotCLEANscore | Function to generate a diagnostic plot using the CLEAN score |
| qvalue | Estimate the q-values for a given set of p-values |
| r2cdt | Functions to generate fTreeView files |
| RandomSet | Testing GO terms, KEGG pathways, and other categories with... |
