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

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

Author
L. Goff, C. Trapnell, D. Kelley
Date of publication
None
Maintainer
Loyal A. Goff <lgoff@csail.mit.edu>
License
Artistic-2.0
Version
2.16.0

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

Files in this package

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