NAMESPACE

# Generated by roxygen2: do not edit by hand

export(GRanges_to_underscored_pos)
export(HiCNVserver)
export(averageMatrixEdges)
export(calcCNVKernelProbDist)
export(calcVecLMs)
export(createChromosomalMatrixSet)
export(downsample_genomic_matrix)
export(extractNegLogPval)
export(formSampleMatrixFromRawGDCData)
export(freadGDCfile)
export(getAnnotationMatrix)
export(getAsymmetricBlockIndices)
export(getBlockAverageMatrixFromBreakpoints)
export(getGlobalRescalingStats)
export(getInterchromosomalInteractivePlot)
export(importBreakpointBed)
export(mathead)
export(postProcessLinRegMatrix)
export(rebinGenomicInteractions)
export(runHiCNVShiny)
export(signedRescale)
export(underscored_pos_to_GRanges)
export(writeAsymmetricMeltedChromosomalMatrixToDisk)
export(writeMeltedChromosomalMatrixToDisk)
import(GenomicFeatures ,except = show)
import(GenomicInteractions)
import(OpenImageR)
import(RCurl, except = reset)
import(circlize, except = degree)
import(data.table, except = c(melt, dcast))
import(doParallel)
import(foreach)
import(ggplot2)
import(htmltools)
import(htmlwidgets)
import(igraph, except = c(decompose, spectrum, groups))
import(jointseg)
import(logging)
import(magrittr)
import(matrixStats)
import(parallel)
import(plotly, except = c(last_plot,select,filter))
import(reshape2)
import(rslurm)
import(shiny, except = runExample)
import(shinycssloaders)
import(shinyjs, except = runExample)
import(shinythemes)
import(spatialfil)
import(stats)
import(visNetwork)
importFrom(BiocManager,repositories)
importFrom(GenomicInteractions,anchorOne)
importFrom(GenomicInteractions,anchorTwo)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,mcols)
importFrom(GenomicRanges,nearest)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,tileGenome)
importFrom(HiCseg,HiCseg_linkC_R)
importFrom(IRanges,IRanges)
importFrom(IRanges,mergeByOverlaps)
importFrom(IRanges,subsetByOverlaps)
importFrom(InteractionSet,findOverlaps)
importFrom(Matrix,bandSparse)
importFrom(Matrix,colMeans)
importFrom(Matrix,rowMeans)
importFrom(Matrix,sparseMatrix)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,mcols)
importFrom(biomaRt,getBM)
importFrom(biomaRt,useMart)
importFrom(data.table,fread)
importFrom(dplyr,bind_cols)
importFrom(foreach,foreach)
importFrom(ggplot2,scale_fill_gradient2)
importFrom(heatmaply,heatmaply)
importFrom(jointseg,jointSeg)
importFrom(plyr,ddply)
importFrom(plyr,ldply)
importFrom(reshape2,colsplit)
importFrom(rtracklayer,import.bed)
importFrom(spatialfil,applyFilter)
importFrom(tidyr,drop_na)
importFrom(tidyr,unite)
importFrom(utils,head)