Package: IsoformSwitchAnalyzeR 2.13.0

Kristoffer Vitting-Seerup

IsoformSwitchAnalyzeR: Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNA-seq (short/long) by tools such as Kallisto, Salmon, StringTie, Tallon, IsoQuant etc.

Authors:Kristoffer Vitting-Seerup [cre, aut], Chunxu Han [ctb], Jeroen Gilis [ctb], Elena Iriondo Delgado [ctb]

IsoformSwitchAnalyzeR_2.13.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
IsoformSwitchAnalyzeR/json (API)

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

Bug tracker:https://github.com/kvittingseerup/isoformswitchanalyzer/issues

Datasets:

On BioConductor:IsoformSwitchAnalyzeR-2.13.0(bioc 3.24)IsoformSwitchAnalyzeR-2.12.0(bioc 3.23)

geneexpressiontranscriptionalternativesplicingdifferentialexpressiondifferentialsplicingvisualizationstatisticalmethodtranscriptomevariantbiomedicalinformaticsfunctionalgenomicssystemsbiologytranscriptomicsrnaseqannotationfunctionalpredictiongenepredictiondataimportmultiplecomparisonbatcheffectimmunooncology

9.07 score 133 stars 405 scripts 16 mentions 52 exports 141 dependencies

Last updated from:2ecfc15e5c. Checks:1 WARNING, 12 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING290
linux-devel-arm64ERROR762
linux-devel-x86_64ERROR863
source / vignettesERROR583
linux-release-arm64ERROR710
linux-release-x86_64ERROR665
macos-release-arm64ERROR576
macos-release-x86_64ERROR989
macos-oldrel-arm64ERROR476
macos-oldrel-x86_64ERROR1046
windows-develERROR867
windows-releaseERROR808
windows-oldrelERROR854
wasm-releaseOK254

Exports:addORFfromGTFanalyzeAlternativeSplicinganalyzeCPATanalyzeCPC2analyzeDeepLoc2analyzeDeepTMHMManalyzeIntronRetentionanalyzeIUPred2AanalyzeNetSurfP3analyzeNovelIsoformORFanalyzeORFanalyzePFAManalyzeSignalPanalyzeSwitchConsequencesexportToPairedGSEAextractConsequenceEnrichmentextractConsequenceEnrichmentComparisonextractConsequenceGenomeWideextractConsequenceSummaryextractGeneExpressionextractGenomeWideAnalysisextractSequenceextractSplicingEnrichmentextractSplicingEnrichmentComparisonextractSplicingGenomeWideextractSplicingSummaryextractSubCellShiftsextractSwitchOverlapextractSwitchSummaryextractTopSwitchesimportCufflinksFilesimportGTFimportIsoformExpressionimportPairedGSEAimportRdataimportSalmonDataisoformSwitchAnalysisCombinedisoformSwitchAnalysisPart1isoformSwitchAnalysisPart2isoformSwitchTestDEXSeqisoformSwitchTestSatuRnisoformToGeneExpisoformToIsoformFractionpreFilterprepareSalmonFileDataFramesubsetSwitchAnalyzeRlistswitchPlotswitchPlotGeneExpswitchPlotIsoExpswitchPlotIsoUsageswitchPlotTopSwitchesswitchPlotTranscript

Dependencies:abindannotateAnnotationDbiAnnotationFilterAnnotationHubaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbitbit64bitopsblobbootBSgenomecachemcigarilloclicliprcodetoolscpp11crayoncurlDBIdbplyrDelayedArrayDESeq2DEXSeqdplyredgeRensembldbfarverfastmapfilelockformatRfutile.loggerfutile.optionsgenefiltergeneplottergenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehmshttrhttr2hwriterIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclelimmalocfdrlocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeopensslpbapplypfamAnalyzeRpillarpkgconfigplyrpngprettyunitsprogressProtGenericspurrrpwalignR6rappdirsRColorBrewerRcppRcppArmadilloRCurlreadrreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7satuRnscalesSeqinfosnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsvasystibbletidyrtidyselecttxdbmakertximetatximporttzdbUCSC.utilsutf8vctrsVennDiagramviridisLitevroomwithrXMLxml2xtableXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Add CDS from a GTF file to a switchAnalyzeRlist.addORFfromGTF
Analyse alternative splicing (including intron retention(s))analyzeAlternativeSplicing analyzeIntronRetention
Import Result of External Sequence AnalysisanalyzeCPAT
Import Result of External Sequence AnalysisanalyzeCPC2
Import Result of DeepLoc2 AnalysisanalyzeDeepLoc2
Import Result of a DeepTMHMM analysisanalyzeDeepTMHMM
Import Result of IUPred2A or IUPred3 analysisanalyzeIUPred2A
Import Result of NetSurfP3 analysisanalyzeNetSurfP3
Prediction of Isoform Open Reading Frames.analyzeNovelIsoformORF
Prediction of Transcript Open Reading Frame.analyzeORF
Import Result of PFAM analysisanalyzePFAM
Import Result of SignalP AnalysisanalyzeSignalP
Analyze Consequences of Isoform SwitchesanalyzeSwitchConsequences
Create a switchAnalyzeRlist ObjectcreateSwitchAnalyzeRlist switchAnalyzeRlist switchAnalyzeRlist-class
Example data for IsoformSwitchAnalyzeRexampleSwitchList exampleSwitchListAnalyzed exampleSwitchListIntermediary
Export Data for pairedGSEA AnalysisexportToPairedGSEA
Analyze data for enrichment of specific consequencesextractConsequenceEnrichment
Compare enrichment of specific consequences between comparisonsextractConsequenceEnrichmentComparison
Genome wide Analysis of Consequences due to isoform switchingextractConsequenceGenomeWide extractGenomeWideAnalysis
Analyze Switch ConsequencesextractConsequenceSummary
Extract raw gene counts or abundances from a switchAnalyzeRlist object.extractGeneExpression
Extract nucloetide (and amino acid) sequence of transcripts.extractSequence
Analyze data for enrichment of specific type of alternative splicingextractSplicingEnrichment
Compare enrichment of specific type of alternative splicing between comparisonsextractSplicingEnrichmentComparison
Genome wide Analysis of alternative splicingextractSplicingGenomeWide
Extracts alternative splicing summaryextractSplicingSummary
Global overview of sub-cellular location changesextractSubCellShifts
Visualize Switch OverlapextractSwitchOverlap
Summarize Isoform Switches test Result.extractSwitchSummary
Extract Top Isoform Switches.extractTopSwitches
Import CuffDiff (Cufflinks) Data Into RimportCufflinksFiles
Import Transcripts from a GTF file into RimportGTF
Import expression data from Kallisto, Salmon, RSEM or StringTie into R.importIsoformExpression
Import PairedGSEA Results into IsoformSwitchAnalyzeRimportPairedGSEA
Create SwitchAnalyzeRlist From Standard R ObjectsimportRdata
Direct creation of a switchAnalyzeRlist from Salmon quantificationimportSalmonData
Isoform Switch Analysis Workflow: Extract, Annotate and Visualize all Significant Isoform SwitchesisoformSwitchAnalysisCombined
Isoform Switch Analysis Workflow Part 1: Extract Isoform Switches and Their Bio-sequencesisoformSwitchAnalysisPart1
Isoform Switch Analysis Workflow Part 2: Plot All Isoform Switches and Their AnnotationisoformSwitchAnalysisPart2
Statistical Test for identifying Isoform Switching via DEXSeqisoformSwitchTestDEXSeq
Statistical Test for identifying Isoform Switching via satuRn.isoformSwitchTestSatuRn
Sum transcript/isoform expression to gene get level expression.isoformToGeneExp
Calculate isoform fraction from isoform abundance matrixisoformToIsoformFraction
Filtering of a switchAnalyzeRlistpreFilter
Prepare data.frame needed run importSalmonData.prepareSalmonFileDataFrame
A function which subset all entries in a switchAnalyzeRlist.subsetSwitchAnalyzeRlist
Isoform Switch Analysis PlotswitchPlot
Plots for Analyzing Expression and Isoform UsageswitchPlotGeneExp switchPlotIsoExp switchPlotIsoUsage
Creating the Isoform Switch Analysis Plot for the Top SwitchesswitchPlotTopSwitches
Plot Transcript Structure and AnnotationswitchPlotTranscript