IsoformSwitchAnalyzeR

This is the released version of IsoformSwitchAnalyzeR; for the devel version, see IsoformSwitchAnalyzeR.

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

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DOI: 10.18129/B9.bioc.IsoformSwitchAnalyzeR

Bioconductor version: Release (3.22)

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] ORCID iD ORCID: 0000-0002-6450-0608 , Jeroen Gilis [ctb] ORCID iD ORCID: 0000-0001-8415-0943

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

Version 2.10.0

In Bioconductor since BioC 3.6 (R-3.4) (8 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, Seqinfo, 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, pwalign

System Requirements

URL http://bioconductor.org/packages/IsoformSwitchAnalyzeR/

Bug Reports https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues

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_2.10.0.tar.gz

Windows Binary (x86_64) IsoformSwitchAnalyzeR_2.9.1.zip

macOS Binary (x86_64) IsoformSwitchAnalyzeR_2.10.0.tgz

macOS Binary (arm64) IsoformSwitchAnalyzeR_2.10.0.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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