/usr/lib/R/site-library/cummeRbund/INDEX is in r-bioc-cummerbund 2.6.1-1.
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 | CuffData-class Class "CuffData"
CuffDist-class Class "CuffDist"
CuffFeature-class Class "CuffFeature"
CuffFeatureSet-class Class "CuffFeatureSet"
CuffGene-class Class "CuffGene"
CuffGeneSet-class Class "CuffGeneSet"
CuffSet-class Class "CuffSet"
JSdist Jensen-Shannon distance on columns
JSdistFromP Jensen-Shannon distance on rows from a
pre-defined vector of probabilities
JSdistVec JSdistVec
MAplot MAplot
MDSplot Dimensionality reduction utilities
PINK1 PINK1
addFeatures addFeatures
count-methods Retrieve count values (raw and normalized)
countMatrix countMatrix
csBoxplot csBoxplot
csCluster csCluster
csClusterPlot csClusterPlot
csDendro csDendro
csDensity Density plot of CuffData
csDistHeat csDistHeat
csHeatmap csHeatmap
csScatter Scatter Plot
csSpecificity csSpecificity
csVolcano Volcano Plot
cummeRbund-package cummeRbund: The finishing touch on your Tuxedo
workflow. Analysis, manipulation, and
visualization of Cufflinks HTS data. ~~ package
title ~~
diffData Differential comparison data
dispersionPlot Mean count vs dispersion plot
distValues distValues
expressionBarplot Barplot
expressionPlot Expression Plot
featureNames Feature names
features Features
findGene findGene
findSimilar findSimilar
fpkm-methods Retrieve FPKM values
fpkmMatrix fpkmMatrix
fpkmSCVPlot Quality Control visualizations
getFeatures getFeatures
getGene getGene
getGeneId getGene
getGenes getGenes
getLevels getLevels
getRepLevels getRepLevels
getSig getSig
getSigTable getSigTable
makeprobs Transform a matrix into probabilities by
columns
makeprobsvec makeprobsvec
readCufflinks readCufflinks
repFpkm-methods Retrieve FPKM values
replicates Get replicate sample list from CuffData object
runInfo Retrieve run parameters and information from a
CuffSet object
sampleGeneSet sampleGeneSet
sampleIDs sampleIDs
samples Get sample list from CuffData object
shannon.entropy Shannon entropy
sigMatrix sigMatrix
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