IsoformSwitchAnalyzeR

DOI: 10.18129/B9.bioc.IsoformSwitchAnalyzeR  

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

Bioconductor version: Release (3.17)

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>

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")

 

HTML	R Script	IsoformSwitchAnalyzeR
PDF		Reference Manual
Text		NEWS

Details

biocViews	AlternativeSplicing, Annotation, BatchEffect, BiomedicalInformatics, DataImport, DifferentialExpression, DifferentialSplicing, FunctionalGenomics, FunctionalPrediction, GeneExpression, GenePrediction, ImmunoOncology, MultipleComparison, RNASeq, Software, StatisticalMethod, SystemsBiology, Transcription, TranscriptomeVariant, Transcriptomics, Visualization
Version	2.0.1
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
LinkingTo
Suggests	knitr, BSgenome.Hsapiens.UCSC.hg19, rmarkdown
SystemRequirements
Enhances
URL	http://bioconductor.org/packages/IsoformSwitchAnalyzeR/
BugReports	https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	IsoformSwitchAnalyzeR_2.0.1.tar.gz
Windows Binary	IsoformSwitchAnalyzeR_2.0.1.zip
macOS Binary (x86_64)	IsoformSwitchAnalyzeR_2.0.1.tgz
macOS Binary (arm64)	IsoformSwitchAnalyzeR_2.0.1.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
Old Source Packages for BioC 3.17	Source Archive