Package: cummeRbund 2.54.0

Loyal A. Goff

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.

Authors:L. Goff, C. Trapnell, D. Kelley

cummeRbund_2.54.0.tar.gz
cummeRbund_2.54.0.zip(r-4.7)cummeRbund_2.54.0.zip(r-4.6)cummeRbund_2.54.0.zip(r-4.5)
cummeRbund_2.54.0.tgz(r-4.6-any)cummeRbund_2.54.0.tgz(r-4.5-any)
cummeRbund_2.54.0.tar.gz(r-4.7-any)cummeRbund_2.54.0.tar.gz(r-4.6-any)
cummeRbund_2.54.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
cummeRbund/json (API)
NEWS

# Install 'cummeRbund' in R:
install.packages('cummeRbund', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

highthroughputsequencinghighthroughputsequencingdatarnaseqrnaseqdatageneexpressiondifferentialexpressioninfrastructuredataimportdatarepresentationvisualizationbioinformaticsclusteringmultiplecomparisonsqualitycontrol

3.89 score 258 scripts 698 downloads 83 mentions 70 exports 145 dependencies

Last updated from:023ae64ffc (on RELEASE_3_23). Checks:9 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR246
linux-devel-x86_64ERROR488
source / vignettesERROR366
linux-release-x86_64ERROR537
macos-release-arm64ERROR382
macos-oldrel-arm64ERROR415
windows-develERROR399
windows-releaseERROR382
windows-oldrelERROR371
wasm-releaseOK174

Exports:addFeaturesannotationCDSconditionscountcountMatrixcsBoxplotcsClustercsClusterPlotcsDendrocsDensitycsDistHeatcsFoldChangeHeatmapcsHeatmapcsNMFcsPiecsScattercsScatterMatrixcsSpecificitycsVolcanocsVolcanoMatrixDBdiffDatadiffTabledispersionPlotdistValuesexpressionBarplotexpressionPlotfeatureNamesfeaturesfindGenefindSimilarfpkmfpkmMatrixfpkmSCVPlotgenePlotgenesgetFeaturesgetGenegetGeneIdgetGenesgetLevelsgetRepLevelsgetSiggetSigTableisoformsJSdistJSdistFromPJSdistVecmakeGeneRegionTrackmakeprobsmakeprobsvecmakeRnkMAplotMDSplotPCAplotpromotersreadCufflinksrelCDSrepCountMatrixrepFpkmrepFpkmMatrixreplicatesrunInfosamplesshannon.entropysigMatrixsplicingTSSvarModel

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefarverfastclusterfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpillarpkgconfigplyrpngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrxfunXMLxml2XVectoryaml

Readme and manuals

Help Manual

Help pageTopics
cummeRbund: The finishing touch on your Tuxedo workflow. Analysis, manipulation, and visualization of Cufflinks HTS data. ~~ package title ~~cummeRbund-package cummeRbund
addFeaturesaddFeatures addFeatures,CuffData-method addFeatures,CuffSet-method
Retrieve count values (raw and normalized)count count,CuffData-method count,CuffFeature-method count,CuffFeatureSet-method count-methods
countMatrixcountMatrix countMatrix,CuffData-method countMatrix,CuffFeatureSet-method repCountMatrix repCountMatrix,CuffData-method repCountMatrix,CuffFeatureSet-method
csBoxplotcsBoxplot csBoxplot,CuffData-method
csClustercsCluster csCluster,CuffFeatureSet-method
csClusterPlotcsClusterPlot
csDendrocsDendro csDendro,CuffData-method csDendro,CuffFeatureSet-method
Density plot of CuffDatacsDensity csDensity,CuffData-method csDensity,CuffFeatureSet-method
csDistHeatcsDistHeat csDistHeat,CuffData-method csDistHeat,CuffFeatureSet-method
csHeatmapcsFoldChangeHeatmap csFoldChangeHeatmap,CuffFeatureSet-method csHeatmap csHeatmap,CuffFeatureSet-method
Scatter PlotcsScatter csScatter,CuffData-method csScatter,CuffFeatureSet-method csScatterMatrix csScatterMatrix,CuffData-method
csSpecificitycsSpecificity csSpecificity,CuffData-method csSpecificity,CuffFeatureSet-method
Volcano PlotcsVolcano csVolcano,CuffData-method csVolcano,CuffFeatureSet-method csVolcanoMatrix csVolcanoMatrix,CuffData-method
Class "CuffData"annotation,CuffData-method CuffData-class DB,CuffData-method dim,CuffData-method getFeatures,CuffData-method makeRnk makeRnk,CuffData-method
Class "CuffDist"CuffDist-class DB,CuffDist-method dim,CuffDist-method samples,CuffDist-method
Class "CuffFeature"annotation,CuffFeature-method CuffFeature-class diffData,CuffFeature-method fpkmMatrix,CuffFeature-method length,CuffFeature-method samples,CuffFeature-method
Class "CuffFeatureSet"annotation annotation,CuffFeatureSet-method CuffFeatureSet-class diffData,CuffFeatureSet-method featureNames,CuffFeatureSet-method features,CuffFeatureSet-method length,CuffFeatureSet-method samples,CuffFeatureSet-method
Class "CuffGene"CDS,CuffGene-method csPie csPie,CuffGene-method CuffGene-class genePlot genePlot,CuffGene-method genes,CuffGene-method isoforms,CuffGene-method length,CuffGene-method makeGeneRegionTrack makeGeneRegionTrack,CuffGene-method promoters,CuffGene-method relCDS,CuffGene-method splicing,CuffGene-method TSS,CuffGene-method
Class "CuffGeneSet"CDS,CuffGeneSet-method CuffGeneSet-class genes,CuffGeneSet-method isoforms,CuffGeneSet-method promoters,CuffGeneSet-method relCDS,CuffGeneSet-method splicing,CuffGeneSet-method TSS,CuffGeneSet-method
Class "CuffSet"CDS CDS,CuffSet-method conditions conditions,CuffSet-method CuffSet-class DB DB,CuffSet-method genes genes,CuffSet-method isoforms isoforms,CuffSet-method promoters promoters,CuffSet-method relCDS relCDS,CuffSet-method splicing splicing,CuffSet-method TSS TSS,CuffSet-method varModel varModel,CuffSet-method [,CuffSet-method
Differential comparison datadiffData diffData,CuffData-method diffTable diffTable,CuffData-method diffTable,CuffFeatureSet-method
Dimensionality reduction utilitiesMDSplot MDSplot,CuffData-method MDSplot,CuffFeatureSet-method PCAplot PCAplot,CuffData-method PCAplot,CuffFeatureSet-method
Mean count vs dispersion plotdispersionPlot dispersionPlot,CuffData-method dispersionPlot,CuffSet-method
distValuesdistValues distValues,CuffDist-method
Methods for Exploratory Analysis in cummeRbundcsNMF csNMF,CuffData-method csNMF,CuffFeatureSet-method
BarplotexpressionBarplot expressionBarplot,CuffFeature-method expressionBarplot,CuffFeatureSet-method
Expression PlotexpressionPlot expressionPlot,CuffFeature-method expressionPlot,CuffFeatureSet-method
Feature namesfeatureNames,CuffData-method
Featuresfeatures features,CuffGene-method
findGenefindGene findGene,CuffSet-method
findSimilarfindSimilar findSimilar,CuffSet-method
Retrieve FPKM valuesfpkm fpkm,CuffData-method fpkm,CuffFeature-method fpkm,CuffFeatureSet-method fpkm-methods
fpkmMatrixfpkmMatrix fpkmMatrix,CuffData-method fpkmMatrix,CuffFeatureSet-method repFpkmMatrix repFpkmMatrix,CuffData-method repFpkmMatrix,CuffFeature-method repFpkmMatrix,CuffFeatureSet-method
getFeaturesgetFeatures getFeatures,CuffSet-method
getGenegetGene getGene,CuffSet-method
getGenegetGeneId getGeneId,CuffSet-method
getGenesgetGenes getGenes,CuffSet-method
getLevelsgetLevels getLevels,CuffData-method getLevels,CuffSet-method
getRepLevelsgetRepLevels getRepLevels,CuffData-method getRepLevels,CuffSet-method
getSiggetSig getSig,CuffSet-method
getSigTablegetSigTable getSigTable,CuffSet-method
Jensen-Shannon distance on columnsJSdist
Jensen-Shannon distance on rows from a pre-defined vector of probabilitiesJSdistFromP
JSdistVecJSdistVec
Transform a matrix into probabilities by columnsmakeprobs
makeprobsvecmakeprobsvec
MAplotMAplot MAplot,CuffData-method
PINK1PINK1
Quality Control visualizationsfpkmSCVPlot fpkmSCVPlot,CuffData-method
readCufflinksreadCufflinks
Retrieve FPKM valuesrepFpkm repFpkm,CuffData-method repFpkm,CuffFeature-method repFpkm,CuffFeatureSet-method repFpkm-methods
Get replicate sample list from CuffData objectreplicates replicates,CuffData-method replicates,CuffFeature-method replicates,CuffFeatureSet-method replicates,CuffSet-method
Retrieve run parameters and information from a CuffSet objectrunInfo runInfo,CuffSet-method
sampleGeneSetsampleGeneSet
sampleIDssampleIDs
Get sample list from CuffData objectsamples samples,CuffData-method samples,CuffSet-method
Shannon entropyshannon.entropy
sigMatrixsigMatrix sigMatrix,CuffSet-method