/usr/lib/R/site-library/cummeRbund/NAMESPACE is in r-bioc-cummerbund 2.20.0-1ubuntu1.
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 | import(methods)
#importFrom(graphics, plot)
importFrom(plyr, defaults)
importFrom(BiocGenerics, annotation)
#import(S4Vectors)
importFrom(Biobase, featureNames)
exportClasses(CuffSet,
CuffData,
CuffDist,
CuffFeature,
CuffFeatureSet,
CuffGene,
CuffGeneSet
)
exportMethods(
runInfo,
varModel,
annotation,
genes,
isoforms,
TSS,
CDS,
promoters,
splicing,
relCDS,
fpkm,
repFpkm,
count,
distValues,
csDensity,
csScatter,
csVolcano,
csBoxplot,
csHeatmap,
csFoldChangeHeatmap,
csDistHeat,
csCluster,
csDendro,
MAplot,
dispersionPlot,
csSpecificity,
fpkmMatrix,
repFpkmMatrix,
countMatrix,
repCountMatrix,
diffData,
diffTable,
features,
featureNames,
samples,
replicates,
expressionPlot,
expressionBarplot,
getGene,
getGenes,
getFeatures,
getGeneId,
findGene,
getSig,
getSigTable,
addFeatures,
getLevels,
getRepLevels,
findSimilar,
makeRnk,
genePlot,
makeGeneRegionTrack,
DB,
sigMatrix,
csScatterMatrix,
csVolcanoMatrix,
MDSplot,
PCAplot,
fpkmSCVPlot,
csNMF,
conditions,
csPie
)
export("readCufflinks",
"JSdist",
"JSdistVec",
"JSdistFromP",
"shannon.entropy",
"makeprobs",
"makeprobsvec",
"csClusterPlot"
)
#importClassesFrom("Biobase","Versioned")
#importClassesFrom("Biobase","VersionedBiobase")
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