Introduction | Reading in unaligned and aligned read data | Unaligned reads | Aligned reads | Read-level EDA | Numbers of unaligned and aligned reads | Read quality scores | Individual lane summaries | Read nucleotide distributions | Gene-level EDA | Classes and methods for gene-level counts | Between-lane distribution of gene-level counts | Over-dispersion | Gene-specific effects on read counts | Normalization | Offset | Differential expression analysis | edgeR | DESeq2 | Definitions and conventions | Rounding | Zero counts | Retrieving gene length and GC-content | SessionInfo | References
Package: EDASeq 2.47.0
Davide Risso
EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq
Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).
Authors:
EDASeq_2.47.0.tar.gz
EDASeq_2.47.0.zip(r-4.7)EDASeq_2.47.0.zip(r-4.6)EDASeq_2.47.0.zip(r-4.5)
EDASeq_2.47.0.tgz(r-4.6-any)EDASeq_2.47.0.tgz(r-4.5-any)
EDASeq_2.47.0.tar.gz(r-4.7-any)EDASeq_2.47.0.tar.gz(r-4.6-any)
EDASeq_2.47.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
EDASeq/json (API)
| # Install 'EDASeq' in R: |
| install.packages('EDASeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/drisso/edaseq/issues
Datasets:
- yeastGC - GC-content of _S. Cerevisiae_ genes
- yeastLength - Length of _S. Cerevisiae_ genes
On BioConductor:EDASeq-2.47.0(bioc 3.24)EDASeq-2.46.0(bioc 3.23)
immunooncologysequencingrnaseqpreprocessingqualitycontroldifferentialexpression
Last updated from:f26504eccf. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 303 | ||
| linux-devel-x86_64 | NOTE | 493 | ||
| source / vignettes | OK | 356 | ||
| linux-release-x86_64 | NOTE | 502 | ||
| macos-release-arm64 | NOTE | 265 | ||
| macos-oldrel-arm64 | NOTE | 234 | ||
| windows-devel | NOTE | 401 | ||
| windows-release | NOTE | 371 | ||
| windows-oldrel | NOTE | 369 | ||
| wasm-release | OK | 248 |
Exports:barplotbetweenLaneNormalizationbiasBoxplotbiasPlotboxplotcountscounts<-exprsgetGeneLengthAndGCContentinitializeMDPlotmeanVarPlotnewSeqExpressionSetnormCountsnormCounts<-offstoffst<-plotNtFrequencyplotPCAplotQualityplotRLEwidthwithinLaneNormalization
Dependencies:abindAnnotationDbiaroma.lightaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydeldirdplyrfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesgluehmshttrhttr2hwriterinterpIRangesjpegjsonliteKEGGRESTlambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngprettyunitsprogresspurrrpwalignR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfoShortReadsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXMLxml2XVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Exploratory Data Analysis and Normalization for RNA-Seq data | EDASeq-package EDASeq |
| Methods for Function 'barplot' in Package 'EDASeq' | barplot,BamFile-method barplot,BamFileList-method barplot,FastqFileList-method barplot-methods |
| Methods for Function 'betweenLaneNormalization' in Package 'EDASeq' | betweenLaneNormalization betweenLaneNormalization,matrix-method betweenLaneNormalization,SeqExpressionSet-method betweenLaneNormalization-methods |
| Methods for Function 'biasBoxplot' in Package 'EDASeq' | biasBoxplot biasBoxplot,numeric,numeric,numeric-method biasBoxplot,numeric,numeric-method biasBoxplot-methods |
| Methods for Function 'biasPlot' in Package 'EDASeq' | biasPlot biasPlot,matrix,numeric-method biasPlot,SeqExpressionSet,character-method biasPlot-methods |
| Methods for Function 'boxplot' in Package 'EDASeq' | boxplot,FastqQuality-method boxplot,SeqExpressionSet-method boxplot-methods |
| Get gene length and GC-content | getGeneLengthAndGCContent |
| Methods for Function 'MDPlot' in Package 'EDASeq' | MDPlot MDPlot,matrix,numeric-method MDPlot,SeqExpressionSet,numeric-method MDPlot-methods |
| Methods for Function 'meanVarPlot' in Package 'EDASeq' | meanVarPlot meanVarPlot,SeqExpressionSet-method meanVarPlot-methods |
| Function to create a new 'SeqExpressionSet' object. | newSeqExpressionSet |
| Methods for Function 'plot' in Package 'EDASeq' | plot,BamFileList,FastqFileList-method plot-methods |
| Methods for Function 'plotNtFrequency' in Package 'EDASeq' | plotNtFrequency plotNtFrequency,BamFile-method plotNtFrequency,ShortRead-method plotNtFrequency-methods |
| Methods for Function 'plotPCA' in Package 'EDASeq' | plotPCA plotPCA,matrix-method plotPCA,SeqExpressionSet-method plotPCA-methods |
| Methods for Function 'plotQuality' in Package 'EDASeq' | plotQuality plotQuality,BamFile-method plotQuality,BamFileList-method plotQuality,FastqFileList-method plotQuality-methods |
| Methods for Function 'plotRLE' in Package 'EDASeq' | plotRLE plotRLE,matrix-method plotRLE,SeqExpressionSet-method plotRLE-methods |
| "SeqExpressionSet" class for collections of short reads | counts,SeqExpressionSet-method counts<-,SeqExpressionSet-method exprs,SeqExpressionSet-method exprs<-,SeqExpressionSet,ANY-method initialize,SeqExpressionSet-method normCounts normCounts,SeqExpressionSet-method normCounts<- normCounts<-,SeqExpressionSet,ANY-method normCounts<-,SeqExpressionSet-method offst offst,SeqExpressionSet-method offst<- offst<-,SeqExpressionSet,ANY-method offst<-,SeqExpressionSet-method SeqExpressionSet-class |
| Methods for Function 'withinLaneNormalization' in Package 'EDASeq' | withinLaneNormalization withinLaneNormalization,matrix,numeric-method withinLaneNormalization,SeqExpressionSet,character-method withinLaneNormalization-methods |
| GC-content of _S. Cerevisiae_ genes | yeastGC |
| Length of _S. Cerevisiae_ genes | yeastLength |
