cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Version 2.18.0

Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.

AuthorL. Goff, C. Trapnell, D. Kelley
Bioconductor views Bioinformatics Clustering DataImport DataRepresentation DifferentialExpression GeneExpression HighThroughputSequencing HighThroughputSequencingData Infrastructure MultipleComparisons QualityControl RNAseq RNAseqData Visualization
Date of publicationNone
MaintainerLoyal A. Goff <lgoff@csail.mit.edu>
LicenseArtistic-2.0
Version2.18.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("cummeRbund")

Getting started

Package overview

Popular man pages

csDensity: Density plot of CuffData
csHeatmap: csHeatmap
csScatter: Scatter Plot
csVolcano: Volcano Plot
CuffGeneSet-class: Class "CuffGeneSet"
dispersionPlot: Mean count vs dispersion plot
getSig: getSig
See all...

All man pages Function index File listing

Man pages

addFeatures: addFeatures
count: 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
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"
cummeRbund-package: cummeRbund: The finishing touch on your Tuxedo workflow....
diffData: Differential comparison data
dimensionality: Dimensionality reduction utilities
dispersionPlot: Mean count vs dispersion plot
distValues: distValues
exploratory: Methods for Exploratory Analysis in cummeRbund
expressionBarplot: Barplot
expressionPlot: Expression Plot
featureNames: Feature names
features: Features
findGene: findGene
findSimilar: findSimilar
fpkm: Retrieve FPKM values
fpkmMatrix: fpkmMatrix
getFeatures: getFeatures
getGene: getGene
getGeneId: getGene
getGenes: getGenes
getLevels: getLevels
getRepLevels: getRepLevels
getSig: getSig
getSigTable: getSigTable
JSdist: Jensen-Shannon distance on columns
JSdistFromP: Jensen-Shannon distance on rows from a pre-defined vector of...
JSdistVec: JSdistVec
makeprobs: Transform a matrix into probabilities by columns
makeprobsvec: makeprobsvec
MAplot: MAplot
PINK1: PINK1
QCplots: Quality Control visualizations
readCufflinks: readCufflinks
repFpkm: 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

Functions

CDS Man page
CDS,CuffGene-method Man page
CDS,CuffGeneSet-method Man page
CDS,CuffSet-method Man page
CVdensity Source code
CuffData-class Man page
CuffDist-class Man page
CuffFeature-class Man page
CuffFeatureSet-class Man page
CuffGene-class Man page
CuffGeneSet-class Man page
CuffSet-class Man page
DB Man page
DB,CuffData-method Man page
DB,CuffDist-method Man page
DB,CuffSet-method Man page
JSdist Man page Source code
JSdistFromP Man page Source code
JSdistVec Man page Source code
JSdivVec Source code
MAplot Man page Source code
MAplot,CuffData-method Man page
MDSplot Man page Source code Source code
MDSplot,CuffData-method Man page
MDSplot,CuffFeatureSet-method Man page
PCAplot Man page Source code Source code
PCAplot,CuffData-method Man page
PCAplot,CuffFeatureSet-method Man page
PINK1 Man page
QCTable Source code
TSS Man page
TSS,CuffGene-method Man page
TSS,CuffGeneSet-method Man page
TSS,CuffSet-method Man page
[,CuffSet-method Man page
addFeatures Man page Source code Source code
addFeatures,CuffData-method Man page
addFeatures,CuffSet-method Man page
annotation Man page Source code Source code
annotation,CuffData-method Man page
annotation,CuffFeature-method Man page
annotation,CuffFeatureSet-method Man page
as.GRanges Source code
as.GRangesList Source code
barplot Source code Source code
boxplot Source code
bulk_insert Source code
checkReps Source code
checkSamples Source code Source code
cluster Source code
conditions Man page
conditions,CuffSet-method Man page
confidencePlot Source code
count Man page Source code Source code Source code
count,CuffData-method Man page
count,CuffFeature-method Man page
count,CuffFeatureSet-method Man page
count-methods Man page
countMatrix Man page Source code Source code
countMatrix,CuffData-method Man page
countMatrix,CuffFeatureSet-method Man page
createDB_noIndex Source code
createIndices Source code
csBoxplot Man page
csBoxplot,CuffData-method Man page
csCluster Man page
csCluster,CuffFeatureSet-method Man page
csClusterPlot Man page Source code
csDendro Man page
csDendro,CuffData-method Man page
csDendro,CuffFeatureSet-method Man page
csDensity Man page
csDensity,CuffData-method Man page
csDensity,CuffFeatureSet-method Man page
csDistHeat Man page
csDistHeat,CuffData-method Man page
csDistHeat,CuffFeatureSet-method Man page
csFoldChangeHeatmap Man page
csFoldChangeHeatmap,CuffFeatureSet-method Man page
csHeatmap Man page
csHeatmap,CuffFeatureSet-method Man page
csNMF Man page
csNMF,CuffData-method Man page
csNMF,CuffFeatureSet-method Man page
csPie Man page
csPie,CuffGene-method Man page
csScatter Man page
csScatter,CuffData-method Man page
csScatter,CuffFeatureSet-method Man page
csScatterMatrix Man page
csScatterMatrix,CuffData-method Man page
csSpecificity Man page
csSpecificity,CuffData-method Man page
csSpecificity,CuffFeatureSet-method Man page
csVolcano Man page
csVolcano,CuffData-method Man page
csVolcano,CuffFeatureSet-method Man page
csVolcanoMatrix Man page
csVolcanoMatrix,CuffData-method Man page
cuff2db Source code
cummeRbund Man page
cummeRbund-package Man page
dendro Source code Source code
density Source code Source code
deogram Source code
dfToJSONarray Source code
diffData Man page Source code Source code Source code
diffData,CuffData-method Man page
diffData,CuffFeature-method Man page
diffData,CuffFeatureSet-method Man page
diffTable Man page Source code Source code
diffTable,CuffData-method Man page
diffTable,CuffFeatureSet-method Man page
dim,CuffData-method Man page
dim,CuffDist-method Man page
dispersionPlot Man page Source code Source code
dispersionPlot,CuffData-method Man page
dispersionPlot,CuffSet-method Man page
distValues Man page
distValues,CuffDist-method Man page
distheat Source code Source code
expressionBarplot Man page
expressionBarplot,CuffFeature-method Man page
expressionBarplot,CuffFeatureSet-method Man page
expressionPlot Man page Source code Source code
expressionPlot,CuffFeature-method Man page
expressionPlot,CuffFeatureSet-method Man page
fcheatmap Source code
featureNames Source code Source code
featureNames,CuffData-method Man page
featureNames,CuffFeatureSet-method Man page
features Man page
features,CuffFeatureSet-method Man page
features,CuffGene-method Man page
findGene Man page Source code
findGene,CuffSet-method Man page
findK Source code
findSimilar Man page Source code
findSimilar,CuffSet-method Man page
fpkm Man page Source code Source code Source code
fpkm,CuffData-method Man page
fpkm,CuffFeature-method Man page
fpkm,CuffFeatureSet-method Man page
fpkm-methods Man page
fpkmMatrix Man page Source code Source code Source code
fpkmMatrix,CuffData-method Man page
fpkmMatrix,CuffFeature-method Man page
fpkmMatrix,CuffFeatureSet-method Man page
fpkmSCVPlot Man page Source code
fpkmSCVPlot,CuffData-method Man page
genePlot Man page
genePlot,CuffGene-method Man page
genes Man page
genes,CuffGene-method Man page
genes,CuffGeneSet-method Man page
genes,CuffSet-method Man page
getCountMA Source code
getFeatures Man page Source code
getFeatures,CuffData-method Man page
getFeatures,CuffSet-method Man page
getGene Man page Source code
getGene,CuffSet-method Man page
getGeneId Man page Source code
getGeneId,CuffSet-method Man page
getGenes Man page Source code
getGenes,CuffSet-method Man page
getGenome Source code
getLevels Man page Source code Source code
getLevels,CuffData-method Man page
getLevels,CuffSet-method Man page
getMA Source code
getRepConditionLevels Source code
getRepLevels Man page Source code Source code
getRepLevels,CuffData-method Man page
getRepLevels,CuffSet-method Man page
getSamples Source code
getSamplesFromColnames Source code
getSig Man page Source code
getSig,CuffSet-method Man page
getSigTable Man page Source code
getSigTable,CuffSet-method Man page
ggheat Source code
hclustToJSON Source code
heatmap Source code
isoforms Man page
isoforms,CuffGene-method Man page
isoforms,CuffGeneSet-method Man page
isoforms,CuffSet-method Man page
length,CuffFeature-method Man page
length,CuffFeatureSet-method Man page
length,CuffGene-method Man page
loadCDS Source code
loadGTF Source code
loadGenes Source code
loadIsoforms Source code
loadRepTable Source code
loadRunInfo Source code
loadTSS Source code
loadVarModelTable Source code
makeGRanges Source code
makeGeneRegionTrack Man page Source code
makeGeneRegionTrack,CuffGene-method Man page
makeIdentityMatrix Source code
makeRnk Man page Source code
makeRnk,CuffData-method Man page
makeRnkTest Source code
makeRnkTestStat Source code
makeprobs Man page Source code
makeprobsvec Man page Source code
nmf Source code Source code
pie Source code
plot Source code
plot2 Source code
plotmatrix Source code
populateSampleTable Source code
promoters Man page
promoters,CuffGene-method Man page
promoters,CuffGeneSet-method Man page
promoters,CuffSet-method Man page
ratioCluster Source code
readCufflinks Man page Source code
recordGenome Source code
relCDS Man page
relCDS,CuffGene-method Man page
relCDS,CuffGeneSet-method Man page
relCDS,CuffSet-method Man page
repCountMatrix Man page Source code Source code
repCountMatrix,CuffData-method Man page
repCountMatrix,CuffFeatureSet-method Man page
repFpkm Man page Source code Source code Source code
repFpkm,CuffData-method Man page
repFpkm,CuffFeature-method Man page
repFpkm,CuffFeatureSet-method Man page
repFpkm-methods Man page
repFpkmMatrix Man page Source code Source code Source code
repFpkmMatrix,CuffData-method Man page
repFpkmMatrix,CuffFeature-method Man page
repFpkmMatrix,CuffFeatureSet-method Man page
replicates Man page Source code Source code Source code Source code
replicates,CuffData-method Man page
replicates,CuffFeature-method Man page
replicates,CuffFeatureSet-method Man page
replicates,CuffSet-method Man page
runInfo Man page Source code
runInfo,CuffSet-method Man page
sampleGeneSet Man page
sampleIDs Man page
samples Man page Source code Source code Source code Source code Source code
samples,CuffData-method Man page
samples,CuffDist-method Man page
samples,CuffFeature-method Man page
samples,CuffFeatureSet-method Man page
samples,CuffSet-method Man page
scatter Source code Source code
scatter2 Source code
scatterMat Source code
sensitivityPlot Source code
shannon.entropy Man page Source code
sigMatrix Man page Source code
sigMatrix,CuffSet-method Man page
specificity Source code Source code Source code
splicing Man page
splicing,CuffGene-method Man page
splicing,CuffGeneSet-method Man page
splicing,CuffSet-method Man page
statsMatrix Source code
values Source code
varModel Man page Source code
varModel,CuffSet-method Man page
volcano Source code Source code
volcanoMatrix Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/database-setup.R
R/methods-CuffData.R
R/methods-CuffDist.R
R/methods-CuffFeature.R
R/methods-CuffFeatureSet.R
R/methods-CuffGene.R
R/methods-CuffGeneSet.R
R/methods-CuffSet.R
R/tools.R
README
build
build/vignette.rds
data
data/sampleData.RData
data/sampleData.rda
inst
inst/NEWS
inst/doc
inst/doc/cummeRbund-example-workflow.R
inst/doc/cummeRbund-example-workflow.Rnw
inst/doc/cummeRbund-example-workflow.pdf
inst/doc/cummeRbund-manual.R
inst/doc/cummeRbund-manual.Rnw
inst/doc/cummeRbund-manual.pdf
inst/extdata
inst/extdata/cds.count_tracking
inst/extdata/cds.diff
inst/extdata/cds.fpkm_tracking
inst/extdata/cds.read_group_tracking
inst/extdata/cds_exp.diff
inst/extdata/chr1_snippet.gtf
inst/extdata/cuffData_schema.sql
inst/extdata/gene_exp.diff
inst/extdata/genes.count_tracking
inst/extdata/genes.fpkm_tracking
inst/extdata/genes.read_group_tracking
inst/extdata/isoform_exp.diff
inst/extdata/isoforms.count_tracking
inst/extdata/isoforms.fpkm_tracking
inst/extdata/isoforms.read_group_tracking
inst/extdata/promoters.diff
inst/extdata/read_groups.info
inst/extdata/run.info
inst/extdata/splicing.diff
inst/extdata/tss_group_exp.diff
inst/extdata/tss_groups.count_tracking
inst/extdata/tss_groups.fpkm_tracking
inst/extdata/tss_groups.read_group_tracking
inst/reports
inst/reports/runReport.Rmd
inst/reports/styles
inst/reports/styles/report_style.css
man
man/CuffData-class.Rd
man/CuffDist-class.Rd
man/CuffFeature-class.Rd
man/CuffFeatureSet-class.Rd
man/CuffGene-class.Rd
man/CuffGeneSet-class.Rd
man/CuffSet-class.Rd
man/JSdist.Rd
man/JSdistFromP.Rd
man/JSdistVec.Rd
man/MAplot.Rd
man/PINK1.Rd
man/QCplots.Rd
man/addFeatures.Rd
man/count.Rd
man/countMatrix.Rd
man/csBoxplot.Rd
man/csCluster.Rd
man/csClusterPlot.Rd
man/csDendro.Rd
man/csDensity.Rd
man/csDistHeat.Rd
man/csHeatmap.Rd
man/csScatter.Rd
man/csSpecificity.Rd
man/csVolcano.Rd
man/cummeRbund-package.Rd
man/diffData.Rd
man/dimensionality.Rd
man/dispersionPlot.Rd
man/distValues.Rd
man/exploratory.Rd
man/expressionBarplot.Rd
man/expressionPlot.Rd
man/featureNames.Rd
man/features.Rd
man/findGene.Rd
man/findSimilar.Rd
man/fpkm.Rd
man/fpkmMatrix.Rd
man/getFeatures.Rd
man/getGene.Rd
man/getGeneId.Rd
man/getGenes.Rd
man/getLevels.Rd
man/getRepLevels.Rd
man/getSig.Rd
man/getSigTable.Rd
man/makeprobs.Rd
man/makeprobsvec.Rd
man/readCufflinks.Rd
man/repFpkm.Rd
man/replicates.Rd
man/runInfo.Rd
man/sampleGeneSet.Rd
man/sampleIDs.Rd
man/samples.Rd
man/shannon.entropy.Rd
man/sigMatrix.Rd
vignettes
vignettes/ENCODE_SCV.pdf
vignettes/cuffData_schema.pdf
vignettes/cummeRbund-example-workflow.Rnw
vignettes/cummeRbund-manual.Rnw
cummeRbund documentation built on May 20, 2017, 9:18 p.m.

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