To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

IsoformSwitchAnalyzeR

DOI: 10.18129/B9.bioc.IsoformSwitchAnalyzeR    

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

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

Bioconductor version: Development (3.7)

IsoformSwitchAnalyzeR enabels 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 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 1.1.0
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, tximport, edgeR
LinkingTo
Suggests knitr, BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances
URL http://bioconductor.org/packages/IsoformSwitchAnalyzeR/
BugReports https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package IsoformSwitchAnalyzeR_1.1.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) IsoformSwitchAnalyzeR_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/IsoformSwitchAnalyzeR
Package Short Url http://bioconductor.org/packages/IsoformSwitchAnalyzeR/
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