# Generated by roxygen2: do not edit by hand

export(GBAccession)
export(LDWeaver)
export(analyse_long_range_links)
export(cleanup)
export(create_network)
export(create_network_for_gene)
export(create_tanglegram)
export(estimate_Hamming_distance_weights)
export(estimate_variation_in_CDS)
export(generate_Links_SNPS_fasta)
export(genomewide_LDMap)
export(make_gwes_plots)
export(parse_fasta_SNP_alignment)
export(parse_fasta_alignment)
export(parse_genbank_file)
export(parse_gff_file)
export(perform_MI_computation)
export(perform_snpEff_annotations)
export(read_AnnotatedLinks)
export(read_LongRangeLinks)
export(read_ShortRangeLinks)
export(read_TopHits)
export(snpdat_to_fa)
export(view_tree)
export(write_output_for_gwes_explorer)
exportClasses(GBAccession)
exportClasses(GBKFile)
exportClasses(GenBankFile)
exportClasses(GenBankRecord)
import(GenomicRanges)
importClassesFrom(Biostrings,XStringSet)
importClassesFrom(GenomicRanges,CompressedGRangesList)
importClassesFrom(GenomicRanges,GRangesList)
importFrom(Biostrings,AAString)
importFrom(Biostrings,AAStringSet)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,extractAt)
importFrom(GenomeInfoDb,Seqinfo)
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,width)
importFrom(IRanges,IRanges)
importFrom(IRanges,heads)
importFrom(IRanges,ranges)
importFrom(Matrix,colSums)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,t)
importFrom(Matrix,which)
importFrom(RColorBrewer,brewer.pal)
importFrom(Rcpp,sourceCpp)
importFrom(RcppArmadillo,fastLm)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(VariantAnnotation,VRanges)
importFrom(VariantAnnotation,makeVRangesFromGRanges)
importFrom(ape,read.gff)
importFrom(chromoMap,chromoMap)
importFrom(data.table,"%between%")
importFrom(data.table,.I)
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,setattr)
importFrom(dplyr,`%>%`)
importFrom(dplyr,summarise)
importFrom(fitdistrplus,fitdist)
importFrom(ggplot2,aes)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,scale_colour_gradientn)
importFrom(ggplot2,scale_fill_viridis_d)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_void)
importFrom(ggraph,geom_edge_arc2)
importFrom(ggraph,geom_node_label)
importFrom(ggraph,ggraph)
importFrom(ggraph,scale_edge_colour_discrete)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,png)
importFrom(heatmap3,heatmap3)
importFrom(htmlwidgets,saveWidget)
importFrom(igraph,graph_from_edgelist)
importFrom(igraph,set.edge.attribute)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(parallel,detectCores)
importFrom(plyr,.)
importFrom(plyr,ddply)
importFrom(stats,coef)
importFrom(stats,cutree)
importFrom(stats,dist)
importFrom(stats,fitted)
importFrom(stats,hclust)
importFrom(stats,kmeans)
importFrom(stats,pbeta)
importFrom(stats,quantile)
importFrom(utils,packageVersion)
importFrom(utils,read.table)
importFrom(utils,setTxtProgressBar)
importFrom(utils,stack)
importFrom(utils,timestamp)
importFrom(utils,txtProgressBar)
importFrom(utils,write.table)
importMethodsFrom(MatrixExtra,crossprod)
importMethodsFrom(MatrixExtra,t)
importMethodsFrom(MatrixExtra,tcrossprod)
useDynLib(LDWeaver)
