useDynLib("ArrayExpressHTS")

export("ArrayExpressHTS", "ArrayExpressHTSFastQ", 
        "prepareReference", "prepareAnnotation", 
        "getPipelineOptions", "getPipelineOption", 
        "setPipelineOptions", "isRCloud", 
        "getDefaultProcessingOptions", 
        "getDefaultRCloudOptions", 
        "getDefaultFilteringOptions")

#Generated by codetoolsBioC version 0.0.16
#Timestamp: Mon Apr  4 13:39:26 2011

#Depends: .GlobalEnv, sampling, snow

#Imports: Biobase, Biostrings, DESeq, GenomicRanges, Hmisc, IRanges,
#         R2HTML, RColorBrewer, Rsamtools, ShortRead, XML, biomaRt,
#         edgeR, grDevices, graphics, methods, rJava, stats, svMisc,
#         utils

importMethodsFrom(Biobase, assayData, experimentData, "experimentData<-", 
exprs, "exprs<-", fData, featureData, "featureData<-", featureNames, 
pData, phenoData, "phenoData<-", sampleNames)

importMethodsFrom(Biostrings, alphabetFrequency, quality)

importMethodsFrom(IRanges, Rle, disjointBins, findOverlaps, subseq,
width)

importMethodsFrom(Rsamtools, ScanBamParam, scanBam, scanBamHeader)

importMethodsFrom(ShortRead, FastqQuality, alphabetByCycle, dustyScore,
id, readFastq, srFilter, tables)

importFrom(Biobase, read.AnnotatedDataFrame, estimateSizeFactors)

importFrom(Biostrings, BStringSet, DNAStringSet, fasta.info, readDNAStringSet)

importFrom(DESeq, estimateVarianceFunctions,
nbinomTest, newCountDataSet)

importFrom(GenomicRanges, GRanges)

importFrom(Hmisc, errbar, wtd.var)

importFrom(IRanges, IRanges, RangedData, RangedDataList)

importFrom(R2HTML, HTML, HTMLEndFile, HTMLInitFile, as.title)

importFrom(RColorBrewer, brewer.pal)

importFrom(Rsamtools, scanBamFlag, scanBamWhat)

importFrom(ShortRead, AlignedDataFrame, AlignedRead, nFilter, sread)

importFrom(XML, xmlElementsByTagName, xmlRoot, xmlToList, xmlTreeParse,
xmlValue)

importFrom(biomaRt, getBM, listDatasets, listMarts, useMart)

importFrom(edgeR, calcNormFactors)

importFrom(grDevices, dev.off, dev.print, png, rainbow)

importFrom(graphics, axis, barplot, boxplot, hist, legend, lines, par,
pie, plot, plot.new, plot.window, rect, text, title)

importFrom(methods, as, is, new)

importFrom(rJava, .jinit)

importFrom(stats, density, ecdf, end, quantile, runif, start)

importFrom(svMisc, progress)

importFrom(sendmailR, sendmail, mime_part)

importFrom(utils, assignInNamespace, combn, download.file, read.table,
write.table)

importFrom(bitops, bitAnd)

