## IMPORTS
import(rjson, GenomicRanges, GenomicAlignments, Rsamtools, Biostrings, ShortRead, grid, ggplot2, limma, edgeR, GOstats, GO.db, annotate, pheatmap, BatchJobs, methods)
## S4 Classes
exportClasses(
    "SYSargs", "catDB", "VENNset", "INTERSECTset"
)

## Methods
exportMethods(
    "targetsin", "targetsout", "targetsheader", "modules", "software", "cores", 
    "other", "reference", "results", "infile1", "infile2", "outfile1", "SampleName", 
    "sysargs", "outpaths", "show", "names", "length", "[", "catmap", "catlist", "idconv",
    "setlist", "intersectmatrix", "complexitylevels", "vennlist", "intersectlist",
    "as.list" 
)

## Functions
# exportPattern("^[[:alpha:]]+")
export(
    ## Data sets

    ## Import/exports
    "readComp", "writeTargetsout", "writeTargetsRef", "mergeBamByFactor",

    ## Utilities
    "alignStats", "getQsubargs", "qsubRun", "clusterRun", "returnRPKM", 
    "runCommandline", "systemArgs", "symLink2bam", "moduleload", 
    "modulelist", "run_edgeR", "run_DESeq2", "filterDEGs", "seeFastq", "seeFastqPlot",
    "GOHyperGAll", "GOHyperGAll_Subset", "GOHyperGAll_Simplify", "GOCluster_Report",
    "makeCATdb", "goBarplot", "overLapper", "vennPlot", "olBarplot",
    "preprocessReads", "filterVars", "variantReport", "combineVarReports", 
    "varSummary", "countRangeset", "runDiff"
) 
