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

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
Date of publicationNone
MaintainerLoyal A. Goff <lgoff@csail.mit.edu>
LicenseArtistic-2.0
Version2.16.0

View on Bioconductor

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

addFeatures Man page
addFeatures,CuffData-method Man page
addFeatures,CuffSet-method Man page
annotation Man page
annotation,CuffData-method Man page
annotation,CuffFeature-method Man page
annotation,CuffFeatureSet-method Man page
CDS Man page
CDS,CuffGene-method Man page
CDS,CuffGeneSet-method Man page
CDS,CuffSet-method Man page
conditions Man page
conditions,CuffSet-method Man page
count Man page
count,CuffData-method Man page
count,CuffFeature-method Man page
count,CuffFeatureSet-method Man page
countMatrix Man page
countMatrix,CuffData-method Man page
countMatrix,CuffFeatureSet-method Man page
count-methods Man page
csBoxplot Man page
csBoxplot,CuffData-method Man page
csCluster Man page
csCluster,CuffFeatureSet-method Man page
csClusterPlot Man page
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
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
[,CuffSet-method Man page
cummeRbund Man page
cummeRbund-package Man page
DB Man page
DB,CuffData-method Man page
DB,CuffDist-method Man page
DB,CuffSet-method Man page
diffData Man page
diffData,CuffData-method Man page
diffData,CuffFeature-method Man page
diffData,CuffFeatureSet-method Man page
diffTable Man page
diffTable,CuffData-method Man page
diffTable,CuffFeatureSet-method Man page
dim,CuffData-method Man page
dim,CuffDist-method Man page
dispersionPlot Man page
dispersionPlot,CuffData-method Man page
dispersionPlot,CuffSet-method Man page
distValues Man page
distValues,CuffDist-method Man page
expressionBarplot Man page
expressionBarplot,CuffFeature-method Man page
expressionBarplot,CuffFeatureSet-method Man page
expressionPlot Man page
expressionPlot,CuffFeature-method Man page
expressionPlot,CuffFeatureSet-method Man page
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
findGene,CuffSet-method Man page
findSimilar Man page
findSimilar,CuffSet-method Man page
fpkm Man page
fpkm,CuffData-method Man page
fpkm,CuffFeature-method Man page
fpkm,CuffFeatureSet-method Man page
fpkmMatrix Man page
fpkmMatrix,CuffData-method Man page
fpkmMatrix,CuffFeature-method Man page
fpkmMatrix,CuffFeatureSet-method Man page
fpkm-methods Man page
fpkmSCVPlot Man page
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
getFeatures Man page
getFeatures,CuffData-method Man page
getFeatures,CuffSet-method Man page
getGene Man page
getGene,CuffSet-method Man page
getGeneId Man page
getGeneId,CuffSet-method Man page
getGenes Man page
getGenes,CuffSet-method Man page
getLevels Man page
getLevels,CuffData-method Man page
getLevels,CuffSet-method Man page
getRepLevels Man page
getRepLevels,CuffData-method Man page
getRepLevels,CuffSet-method Man page
getSig Man page
getSig,CuffSet-method Man page
getSigTable Man page
getSigTable,CuffSet-method Man page
isoforms Man page
isoforms,CuffGene-method Man page
isoforms,CuffGeneSet-method Man page
isoforms,CuffSet-method Man page
JSdist Man page
JSdistFromP Man page
JSdistVec Man page
length,CuffFeature-method Man page
length,CuffFeatureSet-method Man page
length,CuffGene-method Man page
makeGeneRegionTrack Man page
makeGeneRegionTrack,CuffGene-method Man page
makeprobs Man page
makeprobsvec Man page
makeRnk Man page
makeRnk,CuffData-method Man page
MAplot Man page
MAplot,CuffData-method Man page
MDSplot Man page
MDSplot,CuffData-method Man page
MDSplot,CuffFeatureSet-method Man page
PCAplot Man page
PCAplot,CuffData-method Man page
PCAplot,CuffFeatureSet-method Man page
PINK1 Man page
promoters Man page
promoters,CuffGene-method Man page
promoters,CuffGeneSet-method Man page
promoters,CuffSet-method Man page
readCufflinks Man page
relCDS Man page
relCDS,CuffGene-method Man page
relCDS,CuffGeneSet-method Man page
relCDS,CuffSet-method Man page
repCountMatrix Man page
repCountMatrix,CuffData-method Man page
repCountMatrix,CuffFeatureSet-method Man page
repFpkm Man page
repFpkm,CuffData-method Man page
repFpkm,CuffFeature-method Man page
repFpkm,CuffFeatureSet-method Man page
repFpkmMatrix Man page
repFpkmMatrix,CuffData-method Man page
repFpkmMatrix,CuffFeature-method Man page
repFpkmMatrix,CuffFeatureSet-method Man page
repFpkm-methods Man page
replicates Man page
replicates,CuffData-method Man page
replicates,CuffFeature-method Man page
replicates,CuffFeatureSet-method Man page
replicates,CuffSet-method Man page
runInfo Man page
runInfo,CuffSet-method Man page
sampleGeneSet Man page
sampleIDs Man page
samples Man page
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
shannon.entropy Man page
sigMatrix Man page
sigMatrix,CuffSet-method Man page
splicing Man page
splicing,CuffGene-method Man page
splicing,CuffGeneSet-method Man page
splicing,CuffSet-method Man page
TSS Man page
TSS,CuffGene-method Man page
TSS,CuffGeneSet-method Man page
TSS,CuffSet-method Man page
varModel Man page
varModel,CuffSet-method Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.