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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(.onAttach)
export(add_alpha)
export(add_array2bed)
export(add_arrayReps2bed)
export(add_rle)
export(align_charLeft)
export(align_charRight)
export(annotate_bed)
export(annotate_blast)
export(are_colors)
export(calc_blkCoords)
export(calc_curvePolygon)
export(calc_pafBlkCoords)
export(check_MCScanXhInstall)
export(check_annotFiles)
export(check_character)
export(check_filePathParam)
export(check_integer)
export(check_logical)
export(check_minimap2install)
export(check_numeric)
export(check_onlyDNA)
export(classify_genome)
export(clean_windows)
export(clus_igraph)
export(convert_input2v1)
export(convert_si2gr)
export(copy_of2results)
export(download_exampleData)
export(find_contigsGapsTelos)
export(find_fewKmers)
export(find_gaps)
export(find_manyKmers)
export(find_nnHit)
export(find_ofFiles)
export(find_runsOfNs)
export(find_selfSyn)
export(find_telomeres)
export(flag_hitsInBlk)
export(flag_hitsInRadius)
export(flag_pafSynteny)
export(get_bedInBlk)
export(get_diamondVersion)
export(get_gappedRanges)
export(get_nAA)
export(get_nSeqs)
export(get_orderedTips)
export(get_orthofinderVersion)
export(ggdotplot)
export(gghits)
export(gs_colors)
export(init_genespace)
export(interp_approx)
export(interp_synPos)
export(join_ranges)
export(match_fasta2gff)
export(minimap_4synteny)
export(nophase_blks)
export(ofInBlk_engine)
export(parse_annotations)
export(parse_faHeader)
export(parse_hogs)
export(parse_ncbi)
export(parse_ogs)
export(parse_orthologues)
export(parse_phytozome)
export(phase_blks)
export(plot_2genomes)
export(plot_contigs)
export(plot_hits)
export(plot_riparian)
export(pull_pairwise)
export(pull_seqInfo)
export(query_cnv)
export(query_hits)
export(query_pangenes)
export(read_aaFasta)
export(read_allBlast)
export(read_bed)
export(read_combBed)
export(read_intSynPos)
export(read_orthofinderSequenceIDs)
export(read_orthofinderSpeciesIDs)
export(read_paf)
export(read_pangenes)
export(read_refGenomeAllBlast)
export(read_refGenomeSynHits)
export(read_synHits)
export(rename_chrs)
export(riparian_engine)
export(round_rect)
export(round_toInteger)
export(run_genespace)
export(run_mcscanx)
export(run_orthofinder)
export(run_orthofinderInBlk)
export(scale_between)
export(set_syntenyParams)
export(slide_genome)
export(subset_bedInGap)
export(subset_minChrSize)
export(syntenic_orthogroups)
export(syntenic_pangenes)
export(synteny)
export(synteny_engine)
export(theme_genespace)
export(window_fasta)
export(write_allBlast)
export(write_combBed)
export(write_intSynPos)
export(write_pangenes)
export(write_synHits)
import(R.utils)
import(data.table)
import(ggplot2)
import(parallel)
importFrom(Biostrings,AAStringSet)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,DNA_ALPHABET)
importFrom(Biostrings,N50)
importFrom(Biostrings,PDict)
importFrom(Biostrings,extractAt)
importFrom(Biostrings,matchPDict)
importFrom(Biostrings,readAAStringSet)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,replaceAt)
importFrom(Biostrings,reverseComplement)
importFrom(Biostrings,seqinfo)
importFrom(Biostrings,vcountPattern)
importFrom(Biostrings,vmatchPattern)
importFrom(Biostrings,width)
importFrom(Biostrings,writeXStringSet)
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(igraph,clusters)
importFrom(igraph,graph_from_data_frame)
importFrom(parallel,detectCores)
importFrom(parallel,mclapply)
importFrom(stats,approx)
importFrom(stats,complete.cases)
importFrom(stats,cor)
importFrom(stats,cutree)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,median)
importFrom(stats,quantile)
importFrom(utils,combn)
importFrom(utils,download.file)
importFrom(utils,head)