GENESPACE/NAMESPACE at dev · Snowseed/GENESPACE · GitHub

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# Generated by roxygen2: do not edit by hand

export(add_alpha)
export(add_arrayRep2gff)
export(add_arrays2gff)
export(add_ofID2gff)
export(add_pepLen2gff)
export(add_rle)
export(add_synChr2gff)
export(add_synOg2gff)
export(annotate_gff)
export(are_colors)
export(blkwise_orthofinder)
export(calc_blkCoords)
export(calc_curvePolygon)
export(calc_partialSw)
export(calc_refChrByGene)
export(check_dropInterSize)
export(check_logicalArg)
export(check_minPepLen)
export(check_orthofinderInstall)
export(choose_mostRecentOF)
export(clus_dbscan)
export(clus_igraph)
export(color_chrBounds)
export(combine_inblkSynOG)
export(complete_subgraph)
export(cosine_points)
export(download_rawData)
export(draw_scaleBar)
export(drop_unusedPeptides)
export(finalize_blocks)
export(find_exampleData)
export(find_globalAnchors)
export(find_hitsInBuff)
export(find_modalValue)
export(find_orthofinderResults)
export(find_rawData)
export(flatten_list)
export(get_hitsInBlks)
export(get_nAA)
export(init_genespace)
export(interp_linear)
export(load_refHits)
export(make_exampleData)
export(make_exampleDataDir)
export(order_filesByMtime)
export(order_synChrs)
export(pangenome)
export(parse_annotations)
export(parse_blast4synteny)
export(parse_faHeader)
export(parse_gff)
export(parse_ncbi)
export(parse_ogs)
export(parse_orthologues)
export(parse_phytozome)
export(pipe_synteny)
export(plot_hits)
export(plot_riparian)
export(prep_ofDbFromPeptide)
export(pull_blkAnchors)
export(pull_nonSelfReg)
export(pull_nonSynOrthologs)
export(pull_pgIntervals)
export(pull_selfRegion)
export(pull_strWidth)
export(pull_synOGs)
export(query_pangenome)
export(read_blast)
export(read_gff)
export(read_orthofinderSequenceIDs)
export(read_orthofinderSpeciesIDs)
export(read_ripHits)
export(reorder_gff)
export(round_rect)
export(round_toInteger)
export(run_mcscanx)
export(run_orthofinder)
export(scale_between)
export(set_syntenyParams)
export(split_blksByRef)
export(split_overlaps)
export(synteny)
export(write_phytozome)
import(R.utils)
import(data.table)
importFrom(Biostrings,AAStringSet)
importFrom(Biostrings,readAAStringSet)
importFrom(Biostrings,width)
importFrom(Biostrings,writeXStringSet)
importFrom(R.utils,gunzip)
importFrom(dbscan,dbscan)
importFrom(dbscan,frNN)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,dev.size)
importFrom(grDevices,pdf)
importFrom(grDevices,rgb)
importFrom(graphics,par)
importFrom(graphics,polygon)
importFrom(graphics,segments)
importFrom(graphics,strheight)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(igraph,clusters)
importFrom(igraph,graph_from_data_frame)
importFrom(parallel,detectCores)
importFrom(parallel,mclapply)
importFrom(rtracklayer,readGFF)
importFrom(stats,complete.cases)
importFrom(stats,cor)
importFrom(stats,median)
importFrom(stats,quantile)
importFrom(utils,download.file)
importFrom(utils,head)