
export("BTreePlotter", trackBTree)
export("BTreePlotter", drawBTree)
export("BTreePlotter", drawBubbles)
export("BTreePlotter", drawFeatures)
export("BTreePredictor", loadRBD)
export("BTreePredictor", btpredict)
export("BTreePredictor", info)
export("Annotate", annoByGenesAndCyto)
export("TrackPlotter", xyTrack)
export("TrackPlotter", bafTrack)
export("TrackPlotter", heteroLociTrack)
export("TrackPlotter", RscoreTrack)
export("TrackPlotter", getTracks)
export("RBD", makeRBD)
export(saveXLS)
export(btcompare)

import("ggplot2")
import("biovizBase")
import("Biobase")
importFrom("grid", unit.pmax)
importFrom("gridExtra", arrangeGrob)
import("gtable")
import("rainbow")
import("WriteXLS")
import("IRanges")
import("GenomicRanges")
import("magrittr")
import("RColorBrewer")
import("BiocStyle")
import("e1071")

importFrom("plyr", l_ply)
importFrom("plyr", llply)
importFrom("plyr", ldply)
importFrom("plyr", dlply)
importFrom("plyr", ddply)
importFrom("plyr", adply)
importFrom("plyr", rename)
importFrom("plyr", mapvalues)
importFrom("plyr", arrange)

importFrom("dplyr", group_by)
importFrom("dplyr", filter)
importFrom("dplyr", summarise)

importFrom("gtools", mixedorder)
importFrom("limma", weighted.median)

# NAMESPACE conflict with ggplot2 2.0 "Position" function
# Must import all BiocGenerics functions manually to suppress warning
importFrom("BiocGenerics",
    clusterCall, clusterApply, clusterApplyLB, clusterEvalQ, 
    clusterExport, clusterMap, clusterSplit,
    parLapply, parSapply, parApply, parRapply, 
    parCapply, parLapplyLB, parSapplyLB,
    updateObject,
    counts, "counts<-",
    design, "design<-",
    dispTable, "dispTable<-",
    sizeFactors, "sizeFactors<-",
    conditions, "conditions<-",
    estimateSizeFactors, 
    estimateDispersions,
    plotDispEsts,
    plotMA,
    plotPCA,
    unstrand,
    annotation, "annotation<-",
    dbconn, dbfile,
    fileName,
    normalize,
    organism, "organism<-",
    species, "species<-",
    score, "score<-",
    strand, "strand<-",
    updateObjectFromSlots,
    getObjectSlots,
    density,
    IQR,
    mad,
    residuals,
    weights,
    xtabs,
    relist,
    boxplot,
    image,
    append,
    as.data.frame,
    as.list,
    as.vector,
    cbind, rbind,
    do.call,
    duplicated, anyDuplicated,
    eval, evalq,
    pmax, pmin, pmax.int, pmin.int,
    Reduce, Filter, Find, Map, 
    # Position, # NAMESPACE conflict with ggplot2 2.0
    get, mget,
    grep, grepl,
    is.unsorted,
    lapply, sapply,
    lengths,
    mapply,
    match,
    nrow, ncol, NROW, NCOL,
    order,
    paste,
    rank,
    rep.int,
    rownames, "rownames<-", colnames, "colnames<-",
    union, intersect, setdiff,
    sort,
    start, "start<-",
    end, "end<-",
    width, "width<-",
    subset,
    table,
    tapply,
    unique,
    unlist,
    unsplit
)


