/usr/lib/R/site-library/Gviz/NAMESPACE is in r-bioc-gviz 1.8.4-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#Timestamp: Tue Feb 14 10:11:41 2012
#Imports: AnnotationDbi, Biobase, BiocGenerics, biomaRt, GenomicRanges,
# graphics, grDevices, grid, IRanges, lattice, methods, RColorBrewer,
# rtracklayer, stats, utils
import(methods)
importClassesFrom(biomaRt, Mart)
importClassesFrom(Biostrings, DNAStringSet, BStringSet, DNAString, BString)
importClassesFrom(GenomicRanges, GRanges)
importClassesFrom(BSgenome, BSgenome, MaskedBSgenome)
importClassesFrom(GenomicFeatures, "TranscriptDb")
importClassesFrom(IRanges, IRanges, NormalIRanges)
importClassesFrom(XVector, GroupedIRanges)
importClassesFrom(rtracklayer, UCSCData)
importMethodsFrom(AnnotationDbi, colnames, get, ls, mget, tail)
importMethodsFrom(Biobase, rowMedians)
importMethodsFrom(BiocGenerics, cbind, duplicated, eval, intersect, lapply,
mapply, order, paste, pmax, pmin, rbind, sapply, setdiff,
table, tapply, unique)
importMethodsFrom(BSgenome, providerVersion)
importMethodsFrom(GenomicFeatures, isActiveSeq, "isActiveSeq<-", exonsBy, transcriptsBy, transcripts)
importMethodsFrom(GenomicRanges, "elementMetadata<-", genome, "genome<-", mcols, "mcols<-",
seqlengths, seqnames, seqlevels, seqinfo, strand, "strand<-",
seqnameStyle, shift)
importMethodsFrom(IRanges, as.data.frame, as.list, as.matrix, as.vector,
"colnames<-", coverage, diff, disjointBins, end, "end<-", range,
findOverlaps, findRun, gsub, ifelse, "%in%", levels, match,
mean, ncol, nrow, queryHits, ranges, "ranges<-", reduce, rev,
Rle, rownames, "rownames<-", runmean, runValue, "runValue<-",
score, sort, split, start, "start<-", sub, subjectHits,
substring, t, tolower, unlist, values, "values<-", which,
which.max, width, "width<-", elementMetadata, endoapply,
elementLengths, overlapsAny)
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)
importFrom(Biobase, listLen, rowMax, rowMin)
importFrom(Biostrings, DNAStringSet, BStringSet, DNAString, BString, reverseComplement, readDNAStringSet, DNA_ALPHABET, stackStrings)
importFrom(BiocGenerics, getObjectSlots)
importFrom(biomaRt, getBM, useMart)
importFrom(GenomicRanges, GRanges, renameSeqlevels)
importFrom(Rsamtools, scanBamFlag, scanBamHeader, scanBam, ScanBamParam, scanFaIndex, scanFa, BamFile, scanBamWhat, bamWhich)
importFrom(graphics, par)
importFrom(grDevices, boxplot.stats, col2rgb, colorRampPalette, extendrange,
hsv, rgb2hsv)
importFrom(grid, convertHeight, convertWidth, convertX, convertY,
current.transform, current.viewport, current.vpTree, dataViewport,
downViewport, gpar, grid.circle, grid.lines, grid.newpage,
grid.polygon, grid.rect, grid.segments, grid.text, grid.yaxis,
popViewport, pushViewport, stringHeight, stringWidth, unit,
upViewport, viewport)
importFrom(IRanges, IRanges, DataFrame)
importFrom(XVector, subseq)
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)
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, head, write.table)
importFrom(GenomicAlignments, extractAlignmentRangesOnReference, sequenceLayer)
###
export(".chrName",
".doCache",
"AlignedReadTrack",
"AlignmentsTrack",
"AnnotationTrack",
"DetailsAnnotationTrack",
"BiomartGeneRegionTrack",
"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")
exportMethods("[",
"as.list",
"chromosome",
"chromosome<-",
"coerce",
"consolidateTrack",
"coords",
"coverage",
"displayPars",
"displayPars<-",
"elementMetadata<-",
"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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