NAMESPACE

import(BiocGenerics)
import(Biobase)
import(methods)
importFrom(biomaRt, useMart, getBM, getSequence)
importFrom(multtest, mt.rawp2adjp)
importFrom(limma, vennCounts,vennDiagram)
importFrom(stats, phyper)
importClassFrom(graph, "graphNEL")
importFrom(graph, ugraph)
importFrom(RBGL, 
           connectedComp)
importFrom(AnnotationDbi, dbconn, select)
importFrom(DBI, dbGetQuery)
importFrom(regioneR, permTest, numOverlaps)
importFrom(BiocInstaller, biocLite)
import(IRanges)
import(Biostrings)
import(BSgenome)
import(GO.db)
import(grid)
import(VennDiagram)
importFrom(ensembldb, disjointExons, genes, exons, transcripts, dbconn)
import(GenomicFeatures)
import(GenomicRanges)
import(GenomeInfoDb)
import(S4Vectors)
importFrom(GenomicAlignments, summarizeOverlaps, Union)
importFrom(SummarizedExperiment, assay, rowRanges, SummarizedExperiment, colData)
importFrom(idr, est.IDR)
importFrom(seqinr, s2c, count, words)
importFrom(matrixStats, rowMins, rowMaxs)
importMethodsFrom(AnnotationDbi, mget, get, mappedkeys, 
                  GOID, Term, Definition, Ontology)
exportClass("bindist", "permPool", "annoGR")
exportMethods("$", "$<-", "info", "annoGR")
export( 
       addAncestors,  
       addGeneIDs,
       addMetadata,
       annoPeaks,
       annotatePeakInBatch, 
       assignChromosomeRegion, 
       BED2RangedData,
       binOverFeature,
       condenseMatrixByColnames, 
       convert2EntrezID,
       countPatternInSeqs,
       egOrgMap,
       featureAlignedDistribution,
       featureAlignedHeatmap,
       featureAlignedSignal,
       findEnhancers,
       findOverlappingPeaks,
       findOverlapsOfPeaks,
       getAllPeakSequence, 
       getAnnotation, 
       getEnrichedGO,
       getEnrichedPATH, 
       getUniqueGOidCount, 
       getVennCounts,
       GFF2RangedData, 
       hyperGtest,
       IDRfilter,
       makeVennDiagram, 
       mergePlusMinusPeaks,
       oligoFrequency,
       oligoSummary,
       peakPermTest,
       peaksNearBDP,
       pie1,
       preparePool,
       reCenterPeaks,
       summarizeOverlapsByBins,
       summarizePatternInPeaks,
       toGRanges, 
       translatePattern,
       write2FASTA,
       xget)