IsoformSwitchAnalyzeR

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see IsoformSwitchAnalyzeR.

An R package to Identify, Annotate and Visualize Isoform Switches with Functional Consequences (from RNA-seq data)


Bioconductor version: 3.7

IsoformSwitchAnalyzeR enables identification and analysis of isoform switches with predicted functional consequences (such as gain/loss of protein domains etc) from quantification by Kallisto, Salmon, Cufflinks/Cuffdiff, RSEM etc.

Author: Kristoffer Vitting-Seerup

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 "3.5") 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

Details

biocViews AlternativeSplicing, Annotation, BiomedicalInformatics, DataImport, DifferentialExpression, DifferentialSplicing, FunctionalGenomics, FunctionalPrediction, GeneExpression, GenePrediction, MultipleComparison, RNASeq, Sequencing, Software, StatisticalMethod, SystemsBiology, Transcription, TranscriptomeVariant, Transcriptomics, Visualization
Version 1.2.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL (>= 2)
Depends R (>= 3.4), cummeRbund
Imports methods, BSgenome, plyr, reshape2, gridExtra, Biostrings, IRanges, GenomicRanges, DRIMSeq, RColorBrewer, rtracklayer, ggplot2, VennDiagram, DBI, grDevices, graphics, stats, utils, GenomeInfoDb, grid, tximport, edgeR, futile.logger
System Requirements
URL http://bioconductor.org/packages/IsoformSwitchAnalyzeR/
Bug Reports https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues
See More
Suggests knitr, BSgenome.Hsapiens.UCSC.hg19
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Package Archives

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

Source Package IsoformSwitchAnalyzeR_1.2.0.tar.gz
Windows Binary IsoformSwitchAnalyzeR_1.2.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) IsoformSwitchAnalyzeR_1.2.0.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/
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Old Source Packages for BioC 3.7 Source Archive