Man pages for uc-bd2k/CLEAN
Clustering Enrichment Analysis

annotateChipSeqPeaksFunction to match each peaks to associated genes in terms of...
bCaSets of p-values derived from two breast cancer data sets.
call.treeviewFunction to call the standalone fTreeView Java application
cdt2rFunctions to import files in TreeView format into R.
chipSeqWeightedSumCalculate binding strengh by summing weighted chip-seq peaks.
CLEAN-packageClustering Enrichment Analysis
cMapA set of p-values derived from the Connectivity Map dataset.
convertFunctionalCategoriesFunction to convert Entrez gene ID-based functional...
createRefGenomeFunction to match download ref genome platform from UCSC.
generateTreeViewFilesWrapper function to perform functional Clustering Enrichment...
geneSigInClusteringAuxiliary functions to funcClustAnnot and geneListEnrichment
genesInEnrichedCategoriesFunction to intersect a gene list with enriched categories
getBinarySubTreeGet the left or right subtree of a given hierarchical...
getFuntionalCategoriesRetrieve functional categories from species-specific library.
gimmOutAn gimmR object, i.e. a list containing a dataframe with gene...
GRSFunction to calculate the Generalized Random Set statistic to...
LRpathTesting GO terms or KEGG with logistic regression
nonHierarchicalClusteringConvert a non-hierarchical clustering into hierarchical...
plotCLEANscoreFunction to generate a diagnostic plot using the CLEAN score
qvalueEstimate the q-values for a given set of p-values
r2cdtFunctions to generate fTreeView files
RandomSetTesting GO terms, KEGG pathways, and other categories with...
uc-bd2k/CLEAN documentation built on Sept. 9, 2017, 10:22 p.m.