# Generated by roxygen2: do not edit by hand

export(calculateCoverageProfile)
export(calculateCoverageProfileFromTxdb)
export(calculateCoverageProfileList)
export(calculateCoverageProfileListFromTxdb)
export(createControlRegions)
export(createOrthologousGeneSetList)
export(extractSequences)
export(getFeatureBoundaryCoverage)
export(getFeatureBoundaryCoverageBin)
export(getMotifSummaryTable)
export(getTargetedGenesTable)
export(getTxdbFeatures)
export(getTxdbFeaturesFromGRanges)
export(importBed)
export(importGtf)
export(parseMsigdb)
export(printMsigdbDataset)
export(queryGff)
export(retrieveOrthologs)
export(runGSEA)
export(runMotifRG)
export(runReport)
export(runTopGO)
export(summarizeQueryRegions)
import(DT)
import(GenomicFeatures)
import(GenomicRanges)
import(knitr)
import(motifRG)
import(org.Hs.eg.db)
import(plotly)
import(rmarkdown)
importFrom(AnnotationDbi,as.list)
importFrom(BSgenome.Hsapiens.UCSC.hg19,Hsapiens)
importFrom(BiocGenerics,unlist)
importFrom(Biostrings,getSeq)
importFrom(GenomeInfoDb,keepStandardChromosomes)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(S4Vectors,Reduce)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(biomaRt,getLDS)
importFrom(biomaRt,useMart)
importFrom(data.table,data.table)
importFrom(data.table,setkey)
importFrom(genomation,ScoreMatrix)
importFrom(genomation,ScoreMatrixBin)
importFrom(org.Hs.eg.db,org.Hs.egENSEMBL2EG)
importFrom(rtracklayer,import.bed)
importFrom(rtracklayer,import.gff)
importFrom(stats,fisher.test)
importFrom(stats,p.adjust)
importFrom(topGO,GenTable)
importFrom(topGO,annFUN.org)
importFrom(topGO,runTest)
importFrom(topGO,usedGO)
