importFrom(foreach, "%dopar%", foreach, getDoParName, getDoParRegistered,
           getDoParWorkers, registerDoSEQ, getDoParVersion)
importFrom(iterators, iter)
importFrom(stats, model.matrix, preplot, rnorm)
importFrom(doRNG, "%dorng%")
importFrom(methods, is)
importClassesFrom(methods, matrix)
import(matrixStats)
import(BiocGenerics)
import(S4Vectors)
importFrom(IRanges,PartitioningByEnd)
importMethodsFrom(IRanges, as.list, as.matrix,
                  diff, distance, distanceToNearest,
                  end, mean,
                  median, nearest, quantile, ranges, reduce,
                  resize, runmed, start,
                  which, which.min, width)
importFrom(IRanges, CharacterList, IRanges)
importFrom(Seqinfo, seqnames)
importFrom(GenomicRanges, GRanges, makeGRangesFromDataFrame)
importMethodsFrom(GenomicRanges, sort)
importFrom(locfit, locfit)
importFrom(locfit, lp)
importFrom(utils, data, packageDescription)
importFrom(parallel, mclapply, stopCluster)
importFrom(GenomicFeatures, exonsBy, cdsBy, transcriptsBy)
importFrom(AnnotationDbi, mappedkeys)
importMethodsFrom(AnnotationDbi, mapIds)

export(bumphunter, bumphunterEngine, clusterMaker, boundedClusterMaker,
       dummyData, getSegments, 
       regionFinder,
       annotateNearest, annotateTranscripts, matchGenes,
       loessByCluster, runmedByCluster, smoother,
       locfitByCluster)
exportMethods(bumphunter)
S3method(print,bumps)
