# Generated by roxygen2: do not edit by hand

export(fromOrthogroups)
export(geneOrderScore)
export(getGeneCluster)
export(getGeneRank)
export(getHomologGeneList)
export(getHomologListForOrthoFinder)
export(grangesFromEnsemblIDs)
export(guessSpecies)
export(homologsFromEnsemblIDs)
export(orthologPairsFromOrthoFinder)
export(plotGeneClusterPatterns)
export(pruningSequences)
importFrom(BiocGenerics,"end<-")
importFrom(BiocGenerics,"start<-")
importFrom(BiocGenerics,"strand<-")
importFrom(BiocGenerics,"width<-")
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,width)
importFrom(Biostrings,AA_PROTEINOGENIC)
importFrom(GenomeInfoDb,keepSeqlevels)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(IRanges,"ranges<-")
importFrom(IRanges,IRanges)
importFrom(IRanges,disjoin)
importFrom(IRanges,distance)
importFrom(IRanges,gaps)
importFrom(IRanges,promoters)
importFrom(IRanges,ranges)
importFrom(IRanges,reduce)
importFrom(IRanges,shift)
importFrom(IRanges,subsetByOverlaps)
importFrom(RANN,nn2)
importFrom(Seqinfo,seqlevels)
importFrom(Seqinfo,seqnames)
importFrom(biomaRt,getBM)
importFrom(biomaRt,listDatasets)
importFrom(biomaRt,useEnsembl)
importFrom(grDevices,palette)
importFrom(grDevices,rainbow)
importFrom(grid,grid.newpage)
importFrom(grid,grid.text)
importFrom(grid,popViewport)
importFrom(grid,pushViewport)
importFrom(grid,viewport)
importFrom(methods,is)
importFrom(methods,new)
importFrom(pwalign,pairwiseAlignment)
importFrom(stats,dist)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(trackViewer,optimizeStyle)
importFrom(trackViewer,setTrackStyleParam)
importFrom(trackViewer,setTrackViewerStyleParam)
importFrom(trackViewer,trackList)
importFrom(trackViewer,viewTracks)
importFrom(utils,adist)
importFrom(utils,combn)
importFrom(utils,read.delim)
