IsoformSwitchAnalyzeR

DOI: 10.18129/B9.bioc.IsoformSwitchAnalyzeR    

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

Bioconductor version: Release (3.12)

IsoformSwitchAnalyzeR enables identification and 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, Cufflinks/Cuffdiff, RSEM etc.

Author: Kristoffer Vitting-Seerup

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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	1.12.0
In Bioconductor since	BioC 3.6 (R-3.4) (3.5 years)
License	GPL (>= 2)
Depends	R (>= 3.5), limma, DEXSeq, ggplot2
Imports	methods, BSgenome, plyr, reshape2, gridExtra, Biostrings(>= 2.50.0), IRanges, GenomicRanges, DRIMSeq, 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
LinkingTo
Suggests	knitr, BSgenome.Hsapiens.UCSC.hg19, cummeRbund
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_1.12.0.tar.gz
Windows Binary	IsoformSwitchAnalyzeR_1.12.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	IsoformSwitchAnalyzeR_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/IsoformSwitchAnalyzeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/IsoformSwitchAnalyzeR
Package Short Url	https://bioconductor.org/packages/IsoformSwitchAnalyzeR/
Package Downloads Report	Download Stats