Package: diffUTR 1.20.0

Pierre-Luc Germain

diffUTR: diffUTR: Streamlining differential exon and 3' UTR usage

The diffUTR package provides a uniform interface and plotting functions for limma/edgeR/DEXSeq -powered differential bin/exon usage. It includes in addition an improved version of the limma::diffSplice method. Most importantly, diffUTR further extends the application of these frameworks to differential UTR usage analysis using poly-A site databases.

Authors:Pierre-Luc Germain [cre, aut], Stefan Gerber [aut]

diffUTR_1.20.0.tar.gz
diffUTR_1.20.0.zip(r-4.7-any)diffUTR_1.20.0.zip(r-4.6-any)diffUTR_1.20.0.zip(r-4.5-any)
diffUTR_1.20.0.tgz(r-4.6-any)diffUTR_1.20.0.tgz(r-4.5-any)
diffUTR_1.20.0.tar.gz(r-4.7-any)diffUTR_1.20.0.tar.gz(r-4.6-any)
diffUTR_1.20.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
diffUTR/json (API)

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

Bug tracker:https://github.com/ethz-ins/diffutr/issues

Datasets:

On BioConductor:diffUTR-1.21.0(bioc 3.24)diffUTR-1.20.0(bioc 3.23)

geneexpression

5.89 score 8 stars 16 scripts 513 downloads 1 mentions 12 exports 129 dependencies

Last updated from:ba87eee6ea (on RELEASE_3_23). Checks:8 NOTE, 2 OK. Indexed: no.

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Exports:addNormalizedAssayscountFeaturesdeuBinPlotDEXSeqWrapperdiffSplice2diffSpliceDGEWrapperdiffSpliceWrappergeneBinHeatmapgeneLevelStatsplotTopGenesprepareBinssimesAggregation

Dependencies:abindannotateAnnotationDbiAnnotationFilteraskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcigarillocirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurlDBIdbplyrDelayedArrayDESeq2DEXSeqdigestdoParalleldplyredgeRensembldbfarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenefiltergeneplottergenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggplot2ggrepelGlobalOptionsgluegtablehmshttrhttr2hwriterIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngprettyunitsprogressProtGenericspurrrR6RColorBrewerRcppRcppArmadilloRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLiteRsubreadrtracklayerS4ArraysS4VectorsS7scalesSeqinfoshapesnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLxml2xtableXVectoryaml

diffUTR
Introduction | Differential exon usage | Differential 3' UTR usage | Getting started | Package installation | Obtaining gene annotations | Workflow for differential exon usage (DEU) analysis | Preparing the annotation | Counting reads in bins | Differential analysis | Workflow for differential 3' UTR usage analysis | Obtaining alternative poly-adenlyation sites and preparing the bins | Counting and differential analysis: | Exploring the results | Top genes | Gene profiles | Overlaying with transcripts
Rendered fromdiffUTR.Rmdusingknitr::rmarkdown

Last update: 2021-05-03
Started: 2021-02-04

diffUTR - diffSplice2
Rendered fromdiffSplice2.Rmdusingknitr::rmarkdown

Last update: 2021-05-03
Started: 2021-05-03

Readme and manuals

Help Manual

Help pageTopics
addNormalizedAssaysaddNormalizedAssays
countFeaturescountFeatures
deuBinPlotdeuBinPlot
diffSplice2diffSplice2
DEUwrappersDEUwrappers DEXSeqWrapper diffSpliceDGEWrapper diffSpliceWrapper
Example bin-level `RangedSummarizedExperiment`example_bin_se
Example gene annotationexample_gene_annotation
geneBinHeatmapgeneBinHeatmap
geneLevelStatsgeneLevelStats
plotTopGenesplotTopGenes
prepareBinsprepareBins
Poly-A sites compendium for Rattus Norvegicus (Rno6)rn6_PAS
simesAggregationsimesAggregation