FindMyFriends/NAMESPACE at master · thomasp85/FindMyFriends · GitHub

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# Generated by roxygen2: do not edit by hand

export("defaults<-")
export("geneNames<-")
export("groupInfo<-")
export("groupNames<-")
export("orgInfo<-")
export("orgNames<-")
export(.fillDefaults)
export(.loadPgExample)
export(addGenomes)
export(addGroupInfo)
export(addOrgInfo)
export(cdhitGrouping)
export(collapseParalogues)
export(defaults)
export(geneLocation)
export(geneNames)
export(geneWidth)
export(genes)
export(getNeighborhood)
export(getRep)
export(gpcGrouping)
export(graphGrouping)
export(groupGenes)
export(groupInfo)
export(groupNames)
export(groupStat)
export(hasGeneGroups)
export(hasGeneInfo)
export(hasParalogueLinks)
export(kmerLink)
export(kmerSimilarity)
export(kmerSplit)
export(manualGrouping)
export(mergePangenomes)
export(nGeneGroups)
export(nGenes)
export(nOrganisms)
export(neighborhoodSplit)
export(orgInfo)
export(orgNames)
export(orgStat)
export(pangenome)
export(pcGraph)
export(pgMatrix)
export(plotEvolution)
export(plotGroup)
export(plotNeighborhood)
export(plotSimilarity)
export(plotStat)
export(plotTree)
export(readAnnot)
export(removeGene)
export(reportGroupChanges)
export(seqToGeneGroup)
export(seqToOrg)
export(setGroupInfo)
export(setOrgInfo)
export(translated)
export(variableRegions)
exportClasses(pgFull)
exportClasses(pgFullLoc)
exportClasses(pgInMem)
exportClasses(pgInMemLoc)
exportClasses(pgLM)
exportClasses(pgLMLoc)
exportClasses(pgSlim)
exportClasses(pgSlimLoc)
exportClasses(pgVirtual)
exportClasses(pgVirtualLoc)
import(BiocGenerics)
import(IRanges)
import(S4Vectors)
import(methods)
importClassesFrom(Biostrings,AAStringSetList)
importClassesFrom(Biostrings,BStringSetList)
importClassesFrom(Biostrings,DNAStringSetList)
importClassesFrom(Biostrings,RNAStringSetList)
importFrom(Biobase,ExpressionSet)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpnworkers)
importFrom(Biostrings,AAStringSet)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,alphabetFrequency)
importFrom(Biostrings,fasta.index)
importFrom(Biostrings,order)
importFrom(Biostrings,readAAStringSet)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,width)
importFrom(Biostrings,writeXStringSet)
importFrom(Matrix,Matrix)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,t)
importFrom(Rcpp,evalCpp)
importFrom(digest,digest)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange_)
importFrom(dplyr,bind_rows)
importFrom(dplyr,do)
importFrom(dplyr,filter_)
importFrom(dplyr,group_by_)
importFrom(dplyr,mutate_)
importFrom(dplyr,n)
importFrom(dplyr,summarise_)
importFrom(dplyr,transmute_)
importFrom(dplyr,ungroup)
importFrom(filehash,dbCreate)
importFrom(filehash,dbExists)
importFrom(filehash,dbFetch)
importFrom(filehash,dbInit)
importFrom(filehash,dbInsert)
importFrom(ggdendro,dendro_data)
importFrom(ggdendro,label)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,coord_polar)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_raster)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplotGrob)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_brewer)
importFrom(ggplot2,scale_fill_distiller)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(grDevices,rgb)
importFrom(grid,grid.draw)
importFrom(grid,grid.newpage)
importFrom(grid,unit)
importFrom(grid,unit.c)
importFrom(gtable,gtable_add_cols)
importFrom(igraph,"E<-")
importFrom(igraph,"V<-")
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,are_adjacent)
importFrom(igraph,as.undirected)
importFrom(igraph,as_data_frame)
importFrom(igraph,bfs)
importFrom(igraph,cluster_edge_betweenness)
importFrom(igraph,cluster_fast_greedy)
importFrom(igraph,cluster_infomap)
importFrom(igraph,cluster_label_prop)
importFrom(igraph,cluster_leading_eigen)
importFrom(igraph,cluster_louvain)
importFrom(igraph,cluster_optimal)
importFrom(igraph,cluster_spinglass)
importFrom(igraph,cluster_walktrap)
importFrom(igraph,components)
importFrom(igraph,degree)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(igraph,graph_from_data_frame)
importFrom(igraph,induced_subgraph)
importFrom(igraph,make_ego_graph)
importFrom(igraph,make_undirected_graph)
importFrom(igraph,membership)
importFrom(igraph,neighbors)
importFrom(igraph,plot.igraph)
importFrom(kebabs,getExRep)
importFrom(kebabs,linearKernel)
importFrom(kebabs,spectrumKernel)
importFrom(reshape2,melt)
importFrom(stats,as.dendrogram)
importFrom(stats,as.dist)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,is.leaf)
importFrom(stats,runif)
importFrom(tools,file_path_sans_ext)
importFrom(utils,combn)
importFrom(utils,flush.console)
importFrom(utils,read.table)
importFrom(utils,unzip)
useDynLib(FindMyFriends)