DOI: 10.18129/B9.bioc.IsoformSwitchAnalyzeR  

This is the development version of IsoformSwitchAnalyzeR; for the stable release version, see IsoformSwitchAnalyzeR.

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

Bioconductor version: Development (3.18)

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 RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.

Author: Kristoffer Vitting-Seerup [cre, aut] , Jeroen Gilis [ctb]

Maintainer: Kristoffer Vitting-Seerup <k.vitting.seerup at>

Citation (from within R, enter citation("IsoformSwitchAnalyzeR")):


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biocViews AlternativeSplicing, Annotation, BatchEffect, BiomedicalInformatics, DataImport, DifferentialExpression, DifferentialSplicing, FunctionalGenomics, FunctionalPrediction, GeneExpression, GenePrediction, ImmunoOncology, MultipleComparison, RNASeq, Software, StatisticalMethod, SystemsBiology, Transcription, TranscriptomeVariant, Transcriptomics, Visualization
Version 2.1.2
In Bioconductor since BioC 3.6 (R-3.4) (6 years)
License GPL (>= 2)
Depends R (>= 4.2), limma, DEXSeq, satuRn(>= 1.7.0), sva, ggplot2 (>= 3.3.5), pfamAnalyzeR
Imports methods, BSgenome, plyr, reshape2, gridExtra, Biostrings(>= 2.50.0), IRanges, GenomicRanges, RColorBrewer, rtracklayer, VennDiagram, DBI, grDevices, graphics, stats, utils, GenomeInfoDb, grid, tximport(>= 1.7.1), tximeta(>= 1.7.12), edgeR, futile.logger, stringr, dplyr, magrittr, readr, tibble, XVector, BiocGenerics, RCurl, Biobase, SummarizedExperiment, tidyr, S4Vectors, BiocParallel
Suggests knitr, BSgenome.Hsapiens.UCSC.hg19, rmarkdown
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