DOI: 10.18129/B9.bioc.IsoformSwitchAnalyzeR    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see IsoformSwitchAnalyzeR.

An R package to Identify, Annotate and Visualize Isoform Switches with Functional Consequences (from RNA-seq data)

Bioconductor version: 3.7

IsoformSwitchAnalyzeR enables identification and analysis of isoform switches with predicted functional consequences (such as gain/loss of protein domains etc) from quantification by Kallisto, Salmon, Cufflinks/Cuffdiff, RSEM etc.

Author: Kristoffer Vitting-Seerup

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

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biocViews AlternativeSplicing, Annotation, BiomedicalInformatics, DataImport, DifferentialExpression, DifferentialSplicing, FunctionalGenomics, FunctionalPrediction, GeneExpression, GenePrediction, MultipleComparison, RNASeq, Sequencing, Software, StatisticalMethod, SystemsBiology, Transcription, TranscriptomeVariant, Transcriptomics, Visualization
Version 1.2.0
License GPL (>= 2)
Depends R (>= 3.4), cummeRbund
Imports methods, BSgenome, plyr, reshape2, gridExtra, Biostrings, IRanges, GenomicRanges, DRIMSeq, RColorBrewer, rtracklayer, ggplot2, VennDiagram, DBI, grDevices, graphics, stats, utils, GenomeInfoDb, grid, tximport, edgeR, futile.logger
Suggests knitr, BSgenome.Hsapiens.UCSC.hg19
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