# Generated by roxygen2: do not edit by hand

export(CDFfromGTF)
export(CDFfromGTF_Multipath)
export(EventDetection)
export(EventDetectionMultipath)
export(EventDetection_transcriptome)
export(EventPointer)
export(EventPointer_Bootstraps)
export(EventPointer_IGV)
export(EventPointer_RNASeq)
export(EventPointer_RNASeq_IGV)
export(EventPointer_RNASeq_TranRef)
export(EventPointer_RNASeq_TranRef_IGV)
export(Events_ReClassification)
export(FindPrimers)
export(GetPSI_FromTranRef)
export(PSI_Statistic)
export(PrepareBam_EP)
export(Protein_Domain_Enrichment)
export(ResulTable)
export(getbootstrapdata)
import(GenomicRanges)
import(Matrix)
import(SGSeq)
import(SummarizedExperiment)
import(doParallel)
import(foreach)
import(glmnet)
import(iterators)
import(poibin)
import(rhdf5)
importFrom('methods',is)
importFrom(BSgenome,getSeq)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,reverseComplement)
importFrom(GenomeInfoDb,'seqlevelsStyle<-')
importFrom(GenomeInfoDb,`seqlevels<-`)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicFeatures,makeTxDbFromBiomart)
importFrom(GenomicFeatures,makeTxDbFromGFF)
importFrom(GenomicFeatures,makeTxDbFromUCSC)
importFrom(GenomicRanges,granges)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(IRanges,"%over%")
importFrom(IRanges,IQR)
importFrom(IRanges,IRanges)
importFrom(IRanges,disjoin)
importFrom(IRanges,median)
importFrom(IRanges,reduce)
importFrom(IRanges,relist)
importFrom(MASS,Null)
importFrom(MASS,ginv)
importFrom(Matrix,Diagonal)
importFrom(RBGL,connectedComp)
importFrom(S4Vectors,isEmpty)
importFrom(S4Vectors,na.omit)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,split)
importFrom(S4Vectors,subjectHits)
importFrom(abind,abind)
importFrom(affxparser,writeCdf)
importFrom(cobs,cobs)
importFrom(doParallel,registerDoParallel)
importFrom(fgsea,fgsea)
importFrom(foreach,"%dopar%")
importFrom(foreach,foreach)
importFrom(graph,ftM2graphNEL)
importFrom(igraph,all_simple_paths)
importFrom(igraph,as_adj)
importFrom(igraph,as_adjacency_matrix)
importFrom(igraph,as_ids)
importFrom(igraph,clusters)
importFrom(igraph,distances)
importFrom(igraph,graph.data.frame)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(igraph,graph_from_data_frame)
importFrom(limma,contrasts.fit)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,topTable)
importFrom(limma,voom)
importFrom(lpSolve,lp)
importFrom(matrixStats,colCumsums)
importFrom(matrixStats,iqr)
importFrom(matrixStats,rowMaxs)
importFrom(matrixStats,rowMins)
importFrom(matrixStats,rowQuantiles)
importFrom(matrixStats,rowRanks)
importFrom(matrixStats,rowSums2)
importFrom(matrixStats,rowVars)
importFrom(methods,'slot<-')
importFrom(methods,as)
importFrom(methods,new)
importFrom(methods,slot)
importFrom(nnls,nnls)
importFrom(prodlim,row.match)
importFrom(qvalue,qvalue)
importFrom(speedglm,control)
importFrom(speedglm,is.sparse)
importFrom(stats,binomial)
importFrom(stats,coef)
importFrom(stats,dist)
importFrom(stats,dnorm)
importFrom(stats,gaussian)
importFrom(stats,model.matrix)
importFrom(stats,nlminb)
importFrom(stats,pbeta)
importFrom(stats,phyper)
importFrom(stats,pnorm)
importFrom(stats,ppoints)
importFrom(stats,predict)
importFrom(stats,pt)
importFrom(stats,qhyper)
importFrom(stats,qnorm)
importFrom(stats,quantile)
importFrom(stats,rnorm)
importFrom(stats,runif)
importFrom(stats,setNames)
importFrom(stringr,str_count)
importFrom(stringr,str_length)
importFrom(stringr,str_replace)
importFrom(tximport,tximport)
importFrom(utils,combn)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)
importFrom(utils,write.table)
useDynLib(EventPointer,gldist_dgl)
useDynLib(EventPointer,gldist_pgl)
useDynLib(EventPointer,gldist_qdgl)
useDynLib(EventPointer,gldist_qgl)
useDynLib(EventPointer,gldist_rgl)
