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

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

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