import(httr, XML, stringr, MASS, R.utils, data.table, GenomicTools.fileHandler)

importFrom("bamsignals", bamCount)
importFrom("Biostrings", nucleotideSubstitutionMatrix, pairwiseAlignment, subseq)
importFrom("GenomicRanges", GRanges)
importFrom("graphics", axis, lines, plot, polygon, rect, text, par)
importFrom("grDevices", colorRampPalette, dev.off, png)
importFrom("IRanges", IRanges)
importFrom("KernSmooth", bkde)
importFrom("RCurl", getURL, getCurlHandle)
importFrom("Rsamtools", scanFa, scanBam)
importFrom("S4Vectors", DataFrame)
importFrom("seqinr", read.fasta, comp)
importFrom("stats", loess, median, predict, quantile, density)
importFrom("utils", download.file, read.csv, read.table, setTxtProgressBar, txtProgressBar, write.table, sessionInfo)

export(coverageDensity, blastSeq, findSpecies, getEnsgInfo, getGeneLocation, getGeneSeq,
       getSequenceFromNCBI, intersectXMLAnnot, plotCoverage, subDose, subPhased, subGprobs, targetScan, tableSpecies, species, getAnnotation,
       plotHit, getFastaFromBed)
