Package: EDASeq 2.41.0
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_2.41.0.tar.gz
EDASeq_2.41.0.zip(r-4.5)EDASeq_2.41.0.zip(r-4.4)EDASeq_2.41.0.zip(r-4.3)
EDASeq_2.41.0.tgz(r-4.4-any)EDASeq_2.41.0.tgz(r-4.3-any)
EDASeq_2.41.0.tar.gz(r-4.5-noble)EDASeq_2.41.0.tar.gz(r-4.4-noble)
EDASeq_2.41.0.tgz(r-4.4-emscripten)EDASeq_2.41.0.tgz(r-4.3-emscripten)
EDASeq.pdf |EDASeq.html✨
EDASeq/json (API)
NEWS
| # 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
- yeastGC - GC-content of _S. Cerevisiae_ genes
- yeastLength - Length of _S. Cerevisiae_ genes
On BioConductor:EDASeq-2.41.0(bioc 3.21)EDASeq-2.40.0(bioc 3.20)
immunooncologysequencingrnaseqpreprocessingqualitycontroldifferentialexpression
Last updated 2 months agofrom:68d2ebaba6. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Nov 29 2024 |
| R-4.3-win | NOTE | Nov 29 2024 |
| R-4.3-mac | NOTE | Nov 29 2024 |
Exports:barplotbetweenLaneNormalizationbiasBoxplotbiasPlotboxplotcountscounts<-exprsgetGeneLengthAndGCContentinitializeMDPlotmeanVarPlotnewSeqExpressionSetnormCountsnormCounts<-offstoffst<-plotNtFrequencyplotPCAplotQualityplotRLEwidthwithinLaneNormalization
Dependencies:abindAnnotationDbiaroma.lightaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydeldirdigestdplyrfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehmshttrhttr2hwriterinterpIRangesjpegjsonliteKEGGRESTlambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrpwalignR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsShortReadsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXMLxml2XVectoryamlzlibbioc
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 |
