Package: cummeRbund 2.49.0

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

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cummeRbund.pdf |cummeRbund.html✨
cummeRbund/json (API)
NEWS

# Install 'cummeRbund' in R:

install.packages('cummeRbund', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

PINK1 - PINK1
sampleGeneSet - SampleGeneSet
sampleIDs - SampleIDs

On BioConductor:cummeRbund-2.47.0(bioc 3.20)cummeRbund-2.46.0(bioc 3.19)

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

highthroughputsequencing highthroughputsequencingdata rnaseq rnaseqdata geneexpression differentialexpression infrastructure dataimport datarepresentation visualization bioinformatics clustering multiplecomparisons qualitycontrol

4.92 score 209 scripts 582 downloads 70 exports 150 dependencies

Last updated 23 days agofrom:ddf62c2f38. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	WARNING	Oct 30 2024
R-4.5-linux	WARNING	Oct 30 2024
R-4.4-win	WARNING	Oct 30 2024
R-4.4-mac	WARNING	Oct 31 2024
R-4.3-win	WARNING	Oct 30 2024
R-4.3-mac	WARNING	Oct 31 2024

Exports:addFeatures annotation CDS conditions count countMatrix csBoxplot csCluster csClusterPlot csDendro csDensity csDistHeat csFoldChangeHeatmap csHeatmap csNMF csPie csScatter csScatterMatrix csSpecificity csVolcano csVolcanoMatrix DB diffData diffTable dispersionPlot distValues expressionBarplot expressionPlot featureNames features findGene findSimilar fpkm fpkmMatrix fpkmSCVPlot genePlot genes getFeatures getGene getGeneId getGenes getLevels getRepLevels getSig getSigTable isoforms JSdist JSdistFromP JSdistVec makeGeneRegionTrack makeprobs makeprobsvec makeRnk MAplot MDSplot PCAplot promoters readCufflinks relCDS repCountMatrix repFpkm repFpkmMatrix replicates runInfo samples shannon.entropy sigMatrix splicing TSS varModel

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr ensembldb evaluate fansi farver fastcluster fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl pillar pkgconfig plogr plyr png prettyunits progress ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xml2 XVector yaml zlibbioc

CummeRbund User Guide

Rendered fromcummeRbund-manual.Rnwusingutils::Sweaveon Oct 30 2024.

Last update: 2017-08-10
Started: 2013-11-01

Sample cummeRbund workflow

Rendered fromcummeRbund-example-workflow.Rnwusingutils::Sweaveon Oct 30 2024.

Last update: 2013-11-01
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
cummeRbund: The finishing touch on your Tuxedo workflow. Analysis, manipulation, and visualization of Cufflinks HTS data. ~~ package title ~~	cummeRbund-package cummeRbund
addFeatures	addFeatures addFeatures,CuffData-method addFeatures,CuffSet-method
Retrieve count values (raw and normalized)	count count,CuffData-method count,CuffFeature-method count,CuffFeatureSet-method count-methods
countMatrix	countMatrix countMatrix,CuffData-method countMatrix,CuffFeatureSet-method repCountMatrix repCountMatrix,CuffData-method repCountMatrix,CuffFeatureSet-method
csBoxplot	csBoxplot csBoxplot,CuffData-method
csCluster	csCluster csCluster,CuffFeatureSet-method
csClusterPlot	csClusterPlot
csDendro	csDendro csDendro,CuffData-method csDendro,CuffFeatureSet-method
Density plot of CuffData	csDensity csDensity,CuffData-method csDensity,CuffFeatureSet-method
csDistHeat	csDistHeat csDistHeat,CuffData-method csDistHeat,CuffFeatureSet-method
csHeatmap	csFoldChangeHeatmap csFoldChangeHeatmap,CuffFeatureSet-method csHeatmap csHeatmap,CuffFeatureSet-method
Scatter Plot	csScatter csScatter,CuffData-method csScatter,CuffFeatureSet-method csScatterMatrix csScatterMatrix,CuffData-method
csSpecificity	csSpecificity csSpecificity,CuffData-method csSpecificity,CuffFeatureSet-method
Volcano Plot	csVolcano 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 data	diffData diffData,CuffData-method diffTable diffTable,CuffData-method diffTable,CuffFeatureSet-method
Dimensionality reduction utilities	MDSplot MDSplot,CuffData-method MDSplot,CuffFeatureSet-method PCAplot PCAplot,CuffData-method PCAplot,CuffFeatureSet-method
Mean count vs dispersion plot	dispersionPlot dispersionPlot,CuffData-method dispersionPlot,CuffSet-method
distValues	distValues distValues,CuffDist-method
Methods for Exploratory Analysis in cummeRbund	csNMF csNMF,CuffData-method csNMF,CuffFeatureSet-method
Barplot	expressionBarplot expressionBarplot,CuffFeature-method expressionBarplot,CuffFeatureSet-method
Expression Plot	expressionPlot expressionPlot,CuffFeature-method expressionPlot,CuffFeatureSet-method
Feature names	featureNames,CuffData-method
Features	features features,CuffGene-method
findGene	findGene findGene,CuffSet-method
findSimilar	findSimilar findSimilar,CuffSet-method
Retrieve FPKM values	fpkm fpkm,CuffData-method fpkm,CuffFeature-method fpkm,CuffFeatureSet-method fpkm-methods
fpkmMatrix	fpkmMatrix fpkmMatrix,CuffData-method fpkmMatrix,CuffFeatureSet-method repFpkmMatrix repFpkmMatrix,CuffData-method repFpkmMatrix,CuffFeature-method repFpkmMatrix,CuffFeatureSet-method
getFeatures	getFeatures getFeatures,CuffSet-method
getGene	getGene getGene,CuffSet-method
getGene	getGeneId getGeneId,CuffSet-method
getGenes	getGenes getGenes,CuffSet-method
getLevels	getLevels getLevels,CuffData-method getLevels,CuffSet-method
getRepLevels	getRepLevels getRepLevels,CuffData-method getRepLevels,CuffSet-method
getSig	getSig getSig,CuffSet-method
getSigTable	getSigTable getSigTable,CuffSet-method
Jensen-Shannon distance on columns	JSdist
Jensen-Shannon distance on rows from a pre-defined vector of probabilities	JSdistFromP
JSdistVec	JSdistVec
Transform a matrix into probabilities by columns	makeprobs
makeprobsvec	makeprobsvec
MAplot	MAplot MAplot,CuffData-method
PINK1	PINK1
Quality Control visualizations	fpkmSCVPlot fpkmSCVPlot,CuffData-method
readCufflinks	readCufflinks
Retrieve FPKM values	repFpkm repFpkm,CuffData-method repFpkm,CuffFeature-method repFpkm,CuffFeatureSet-method repFpkm-methods
Get replicate sample list from CuffData object	replicates replicates,CuffData-method replicates,CuffFeature-method replicates,CuffFeatureSet-method replicates,CuffSet-method
Retrieve run parameters and information from a CuffSet object	runInfo runInfo,CuffSet-method
sampleGeneSet	sampleGeneSet
sampleIDs	sampleIDs
Get sample list from CuffData object	samples samples,CuffData-method samples,CuffSet-method
Shannon entropy	shannon.entropy
sigMatrix	sigMatrix sigMatrix,CuffSet-method