IsoformSwitchAnalyzeR

This is thereleased version of IsoformSwitchAnalyzeR; for the devel version, seeIsoformSwitchAnalyzeR.

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

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

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

Citation (from within R, entercitation("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 appropriateBioconductor 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

biocViews	AlternativeSplicing,Annotation,BatchEffect,BiomedicalInformatics,DataImport,DifferentialExpression,DifferentialSplicing,FunctionalGenomics,FunctionalPrediction,GeneExpression,GenePrediction,ImmunoOncology,MultipleComparison,RNASeq,Software,StatisticalMethod,SystemsBiology,Transcription,TranscriptomeVariant,Transcriptomics,Visualization
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
Linking To
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Depends On Me
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Build Report	Build Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source Package	IsoformSwitchAnalyzeR_2.10.0.tar.gz
Windows Binary (x86_64)	IsoformSwitchAnalyzeR_2.10.0.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/
Package Downloads Report	Download Stats

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