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

Bioconductor version: Release (3.23)

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 RNA-seq (short/long) by tools such as Kallisto, Salmon, StringTie, Tallon, IsoQuant etc.

Author: Kristoffer Vitting-Seerup [cre, aut] ORCID: 0000-0002-6450-0608 , Chunxu Han [ctb], Jeroen Gilis [ctb] ORCID: 0000-0001-8415-0943 , Elena Iriondo Delgado [ctb]

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

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

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

Installation

To install this package, start R (version "4.6") 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	2.12.0
In Bioconductor since	BioC 3.6 (R-3.4) (9 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
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	IsoformSwitchAnalyzeR_2.12.0.tar.gz
Windows Binary (x86_64)	IsoformSwitchAnalyzeR_2.12.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	IsoformSwitchAnalyzeR_2.12.0.tgz
macOS Binary (sonoma-arm64)	IsoformSwitchAnalyzeR_2.12.0.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