IsoformSwitchAnalyzeR

DOI: 10.18129/B9.bioc.IsoformSwitchAnalyzeR  

This is the development version of IsoformSwitchAnalyzeR; for the stable release version, see IsoformSwitchAnalyzeR.

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

Bioconductor version: Development (3.18)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("IsoformSwitchAnalyzeR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	AlternativeSplicing, Annotation, BatchEffect, BiomedicalInformatics, DataImport, DifferentialExpression, DifferentialSplicing, FunctionalGenomics, FunctionalPrediction, GeneExpression, GenePrediction, ImmunoOncology, MultipleComparison, RNASeq, Software, StatisticalMethod, SystemsBiology, Transcription, TranscriptomeVariant, Transcriptomics, Visualization
Version	2.1.2
In Bioconductor since	BioC 3.6 (R-3.4) (5.5 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
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Imports Me
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Build Report

Package Archives

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

Source Package
Windows Binary	IsoformSwitchAnalyzeR_2.1.2.zip
macOS Binary (x86_64)	IsoformSwitchAnalyzeR_2.1.2.tgz
macOS Binary (arm64)
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