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IsoformSwitchAnalyzeR

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


Bioconductor version: Release (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 gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("IsoformSwitchAnalyzeR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("IsoformSwitchAnalyzeR")
IsoformSwitchAnalyzeR HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews AlternativeSplicing, Annotation, BatchEffect, BiomedicalInformatics, DataImport, DifferentialExpression, DifferentialSplicing, FunctionalGenomics, FunctionalPrediction, GeneExpression, GenePrediction, ImmunoOncology, MultipleComparison, RNASeq, Software, StatisticalMethod, SystemsBiology, Transcription, TranscriptomeVariant, Transcriptomics, Visualization
Version 2.2.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 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
System Requirements
URL http://bioconductor.org/packages/IsoformSwitchAnalyzeR/
Bug Reports https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues
See More
Suggests knitr, BSgenome.Hsapiens.UCSC.hg19, rmarkdown
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package IsoformSwitchAnalyzeR_2.2.0.tar.gz
Windows Binary IsoformSwitchAnalyzeR_2.2.0.zip
macOS Binary (x86_64) IsoformSwitchAnalyzeR_2.2.0.tgz
macOS Binary (arm64) IsoformSwitchAnalyzeR_2.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/IsoformSwitchAnalyzeR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/IsoformSwitchAnalyzeR
Bioc Package Browser https://code.bioconductor.org/browse/IsoformSwitchAnalyzeR/
Package Short Url https://bioconductor.org/packages/IsoformSwitchAnalyzeR/
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