CLEAN-package |
Clustering Enrichment Analysis |
atr2r |
Functions to import files in TreeView format into R. |
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. |
CLEAN |
Clustering Enrichment Analysis |
cMap |
A set of p-values derived from the Connectivity Map dataset. |
convertFunctionalCategories |
Function to convert Entrez gene ID-based functional categories from one |
convertGeneTable |
Function to convert Entrez gene ID-based functional categories from one |
funcClustAnnot |
Wrapper function to perform functional Clustering Enrichment Analysis |
geneListEnrichment |
Wrapper function to perform functional Clustering Enrichment Analysis |
generateTreeViewFiles |
Wrapper function to perform functional Clustering Enrichment Analysis |
geneSigInClustering |
Auxiliary functions to funcClustAnnot and geneListEnrichment |
geneSigInClustering_nullDistr |
Auxiliary functions to funcClustAnnot and geneListEnrichment |
geneSigInList |
Auxiliary functions to funcClustAnnot and geneListEnrichment |
genesInEnrichedCategories |
Function to intersect a gene list with enriched categories |
getAllClusters |
Auxiliary functions to funcClustAnnot and geneListEnrichment |
getBinarySubTree |
Get the left or right subtree of a given hierarchical clustering. |
getFunctionalCategories |
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 perform |
gtr2r |
Functions to import files in TreeView format into R. |
initializeCategories |
Auxiliary functions to funcClustAnnot and geneListEnrichment |
insertCdt |
Auxiliary functions to funcClustAnnot and geneListEnrichment |
LRpath |
Testing GO terms or KEGG with logistic regression |
nonHierarchicalClustering |
Convert a non-hierarchical clustering into hierarchical tree-structure |
plotCLEANscore |
Function to generate a diagnostic plot using the CLEAN score |
primSetSigInClustering |
Auxiliary functions to funcClustAnnot and geneListEnrichment |
pruneMinFDR |
Auxiliary functions to funcClustAnnot and geneListEnrichment |
qvalue |
Estimate the q-values for a given set of p-values |
r2atr |
Functions to generate fTreeView files |
r2cdt |
Functions to generate fTreeView files |
r2fni |
Functions to generate fTreeView files |
r2gtr |
Functions to generate fTreeView files |
RandomSet |
Testing GO terms, KEGG pathways, and other categories with Random Set |
RS |
Testing GO terms, KEGG pathways, and other categories with Random Set |
runCLEAN |
Wrapper function to perform functional Clustering Enrichment Analysis |
significantCategories |
Auxiliary functions to funcClustAnnot and geneListEnrichment |