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## try http:// if https:// URLs are not supported
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biocLite("IsoformSwitchAnalyzeR")

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IsoformSwitchAnalyzeR

DOI: 10.18129/B9.bioc.IsoformSwitchAnalyzeR    

This is the development version of IsoformSwitchAnalyzeR; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.6)

Since 2010 state-of-the-art bioinformatics tools have allowed researchers to reconstruct and quantify full length transcripts from RNA-seq data. Such geneome wide isoform resolution data has the potential to facilitate both genome wide analysis of alternative isoform usage and identification of isoform switching. Unfortunatly these types of analysis are still only rarely done and/or reported - in fact only 11% of articles analyzing RNA-seq data publised start 2016 performed analy isoform analysis. We hypothesis that there are 3 reasons why RNA-seq data is not used to its full potential: 1) There is still a lack of tools that can identify isoform switches with isoform resolution - thereby identifying the exact isoforms involved in a switch. 2) Although there are many very good tools to perform sequence analysis there is no common framework, which allows for integration of the analysis provided by these tools. 3) There is a lack of tools facilitating easy and article ready visual visualization of isoform switches. To all 3 problems we developed IsoformSwitchAnalyzeR. IsoformSwitchAnalyzeR is an easy to use R package that enableswhich enables statistical identification as well as visualization of isoform switches with predicted functional consequences from RNA-seq data

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("IsoformSwitchAnalyzeR")

Documentation

HTML R Script IsoformSwitchAnalyzeR
PDF   Reference Manual
Text   NEWS

Details

biocViews AlternativeSplicing, Annotation, BiomedicalInformatics, DataImport, DifferentialExpression, DifferentialSplicing, FunctionalGenomics, FunctionalPrediction, GeneExpression, GenePrediction, MultipleComparison, RNASeq, Sequencing, Software, StatisticalMethod, SystemsBiology, Transcription, TranscriptomeVariant, Transcriptomics, Visualization
Version 0.99.11
In Bioconductor since BioC 3.6 (R-3.4)
License GPL (>= 2)
Depends R (>= 3.4), cummeRbund, spliceR
Imports methods, BSgenome, plyr, reshape2, gridExtra, Biostrings, IRanges, GenomicRanges, DRIMSeq, RColorBrewer, rtracklayer, ggplot2, VennDiagram, DBI, grDevices, graphics, stats, utils, GenomeInfoDb, grid
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Suggests knitr, BSgenome.Hsapiens.UCSC.hg19
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Package Archives

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

Package Source IsoformSwitchAnalyzeR_0.99.11.tar.gz
Windows Binary IsoformSwitchAnalyzeR_0.99.11.zip
Mac OS X 10.11 (El Capitan) IsoformSwitchAnalyzeR_0.99.11.tgz
Source Repository git clone https://git.bioconductor.org/packages/IsoformSwitchAnalyzeR
Package Short Url http://bioconductor.org/packages/IsoformSwitchAnalyzeR/
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