/usr/lib/R/site-library/Gviz/NAMESPACE is in r-bioc-gviz 1.14.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 | import(methods)
import(BiocGenerics)
import(S4Vectors)
import(IRanges)
import(XVector)
import(GenomeInfoDb)
import(GenomicRanges)
import(grid)
importClassesFrom(biomaRt, Mart)
importClassesFrom(Biostrings, DNAStringSet, BStringSet, DNAString, BString)
importClassesFrom(BSgenome, BSgenome, MaskedBSgenome)
importClassesFrom(GenomicFeatures, "TxDb")
importClassesFrom(rtracklayer, UCSCData)
importMethodsFrom(AnnotationDbi, colnames, get, ls, mget, tail)
importMethodsFrom(BSgenome, providerVersion)
importMethodsFrom(GenomicFeatures, isActiveSeq, "isActiveSeq<-", exonsBy, transcriptsBy, transcripts)
importMethodsFrom(rtracklayer, chrom, close, getTable, "tableName<-", track,
ucscTableQuery, trackNames, tableNames, import, import.gff,
import.gff1, import.gff2, import.gff3, import.2bit, import.bed15,
import.bw, import.ucsc, import.bed, import.bedGraph, import.chain,
import.wig, seqinfo)
importMethodsFrom(Biostrings, consensusMatrix, consensusString, unmasked, complement)
importFrom(Biobase, listLen, rowMax, rowMin)
importFrom(Biostrings, DNAStringSet, BStringSet, DNAString, BString, reverseComplement, readDNAStringSet, DNA_ALPHABET, stackStrings)
importFrom(biomaRt, getBM, useMart, listDatasets, listAttributes, listFilters)
importFrom(Rsamtools, scanBamFlag, scanBamHeader, scanBam, ScanBamParam, scanFaIndex, scanFa, BamFile, scanBamWhat, bamWhich)
importFrom(graphics, par)
importFrom(digest, digest)
importFrom(grDevices, boxplot.stats, col2rgb, colorRampPalette, extendrange,
hsv, rgb2hsv)
importFrom(lattice, current.panel.limits, panel.abline, panel.grid, panel.lines,
panel.points, panel.polygon, panel.segments, panel.xyplot, panel.text,
trellis.par.get)
importFrom(matrixStats, colMaxs, rowMedians, rowMins)
importFrom(latticeExtra, panel.xyarea, panel.horizonplot)
importFrom(RColorBrewer, brewer.pal)
importFrom(rtracklayer, GenomicData, ucscGenomes, browserSession, BigWigFile, FastaFile, TwoBitFile)
importFrom(stats, loess.smooth)
importFrom(biovizBase, getBioColor)
importFrom(utils, assignInNamespace, browseURL, write.table)
importFrom(GenomicAlignments, extractAlignmentRangesOnReference, sequenceLayer, GAlignments, summarizeJunctions)
###
export(".chrName",
".doCache",
"AlignedReadTrack",
"AlignmentsTrack",
"AnnotationTrack",
"DetailsAnnotationTrack",
"BiomartGeneRegionTrack",
"CustomTrack",
"DataTrack",
"DisplayPars",
"SequenceTrack",
"OverlayTrack",
"drawGD",
"GeneRegionTrack",
"GenomeAxisTrack",
"HighlightTrack",
"IdeogramTrack",
"UcscTrack",
"addScheme",
"as.list",
"availableDefaultMapping",
"availableDisplayPars",
"clearSessionCache",
"exportTracks",
"getScheme",
"plotTracks")
exportClasses("AlignedReadTrack",
"AlignmentsTrack",
"AnnotationTrack",
"DetailsAnnotationTrack",
"BiomartGeneRegionTrack",
"DataTrack",
"DisplayPars",
"GdObject",
"GeneRegionTrack",
"GenomeAxisTrack",
"IdeogramTrack",
"ImageMap",
"NumericTrack",
"RangeTrack",
"SequenceTrack",
"StackedTrack",
"HighlightTrack",
"OverlayTrack",
"CustomTrack")
exportMethods("[",
"as.list",
"chromosome",
"chromosome<-",
"coerce",
"consolidateTrack",
"coords",
"coverage",
"displayPars",
"displayPars<-",
"end",
"end<-",
"exon",
"exon<-",
"feature",
"feature<-",
"gene",
"gene<-",
"genome",
"genome<-",
"getPar",
"group",
"group<-",
"head",
"identifier",
"identifier<-",
"imageMap",
"initialize",
"length",
"max",
"min",
"names",
"names<-",
"position",
"range",
"ranges",
"score",
"seqnames",
"seqlevels",
"seqinfo",
"setPar",
"split",
"stacking",
"stacking<-",
"stacks",
"start",
"start<-",
"strand",
"strand<-",
"subseq",
"subset",
"symbol",
"symbol<-",
"tags",
"tail",
"transcript",
"transcript<-",
"values",
"values<-",
"width",
"width<-")
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