IsoformSwitchAnalyzeR

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

Bioconductor version: Release (3.20)

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 "4.4") 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

biocViews	AlternativeSplicing, Annotation, BatchEffect, BiomedicalInformatics, DataImport, DifferentialExpression, DifferentialSplicing, FunctionalGenomics, FunctionalPrediction, GeneExpression, GenePrediction, ImmunoOncology, MultipleComparison, RNASeq, Software, StatisticalMethod, SystemsBiology, Transcription, TranscriptomeVariant, Transcriptomics, Visualization
Version	2.6.0
In Bioconductor since	BioC 3.6 (R-3.4) (7 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, 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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Build Report	Build Report

Package Archives

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

Source Package	IsoformSwitchAnalyzeR_2.6.0.tar.gz
Windows Binary (x86_64)	IsoformSwitchAnalyzeR_2.6.0.zip
macOS Binary (x86_64)	IsoformSwitchAnalyzeR_2.6.0.tgz
macOS Binary (arm64)	IsoformSwitchAnalyzeR_2.6.0.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