/usr/lib/R/site-library/biovizBase/NAMESPACE is in r-bioc-biovizbase 1.26.0-1.
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 | useDynLib(biovizBase, .registration=TRUE)
## ======================================================================
## Import
## ======================================================================
import(methods)
import(BiocGenerics)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### base packages
###
importFrom(grDevices, colorRampPalette)
importFrom(graphics, par, plot, rect, text)
importFrom(stats, approx, as.formula, asOneSidedFormula, setNames)
importFrom(utils, menu)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Non-bioconductor packages
###
importFrom(RColorBrewer, brewer.pal)
importFrom(scales, dichromat_pal, dscale, expand_range, rescale)
importFrom(Hmisc, bezier)
importFrom(dichromat, colorschemes)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Bioconductor packages
###
import(S4Vectors)
import(IRanges)
import(GenomeInfoDb)
import(GenomicRanges)
import(SummarizedExperiment)
## Biostrings
importFrom(Biostrings, AA_ALPHABET, DNA_ALPHABET, RNA_ALPHABET,
IUPAC_CODE_MAP, AMINO_ACID_CODE)
importMethodsFrom(Biostrings, getSeq, letterFrequency,
letterFrequencyInSlidingView)
## Rsamtools
importClassesFrom(Rsamtools, BamFile)
importFrom(Rsamtools, index, scanBamFlag, PileupFiles, ApplyPileupsParam)
importMethodsFrom(Rsamtools, ScanBamParam, applyPileups, scanBam)
## GenomicAlignments
importFrom(GenomicAlignments, cigar, readGAlignments)
importClassesFrom(GenomicAlignments, GAlignments)
## GenomicFeatures
importClassesFrom(GenomicFeatures, TxDb)
importMethodsFrom(GenomicFeatures, transcripts, cdsBy, cdsByOverlaps, exonsBy,
exonsByOverlaps, isActiveSeq, "isActiveSeq<-", transcripts,
transcriptsByOverlaps)
## AnnotationDbi
importFrom(AnnotationDbi, unlist2, select, mappedRkeys, revmap, toTable)
## VariantAnnotation
importClassesFrom(VariantAnnotation, VRanges)
## AnnotationFilter
importClassesFrom(AnnotationFilter, AnnotationFilter, GRangesFilter,
TxIdFilter)
importFrom(AnnotationFilter, AnnotationFilter, GRangesFilter, TxIdFilter,
AnnotationFilterList, GenenameFilter)
## ensembldb
importMethodsFrom(ensembldb, listColumns, exons, transcripts)
## ======================================================================
## export
## ======================================================================
## color
export(getBioColor,
plotColorLegend,
genBrewerBlindPalInfo,
genDichromatPalInfo,
genBlindPalInfo,
colorBlindSafePal,
blind.pal.info,
brewer.pal.blind.info,
dichromat.pal.blind.info,
estimateCoverage)
## transform
export(transformToCircle,
transformToRectInCircle,
transformToBarInCircle,
transformToSegInCircle,
transformToLinkInCircle,
transformDfToGr,
transformGRangesForEvenSpace)
exportMethods(transformToGenome,transformToDf)
## utils
exportMethods(addStepping,
shrinkageFun,
maxGap,
splitByFacets,
getGaps,
getXScale,
getYLab,
getXLab,
crunch,
mold)
export(isIdeogram, isSimpleIdeogram, getIdeogram, containLetters,
pileupAsGRanges, pileupGRangesAsVariantTable, GCcontent,
showColor, isJunctionRead, isMatchedWithModel,
flatGrl, getIdeoGR, getScale, getFormalNames, subsetArgsByFormals,
parseArgsForAes, parseArgsForNonAes, strip_formula_dots,
is_coord_truncate_gaps, is_coord_genome)
## exportPattern("^[^\\.]")
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