IsoformSwitchAnalyzeR

DOI: 10.18129/B9.bioc.IsoformSwitchAnalyzeR    

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

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

Bioconductor version: Development (3.10)

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>

Citation (from within R, enter citation("IsoformSwitchAnalyzeR")):

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("IsoformSwitchAnalyzeR")

 

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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 1.7.1
In Bioconductor since BioC 3.6 (R-3.4) (2 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), edgeR, futile.logger, stringr, dplyr, magrittr, readr, XVector
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_1.7.1.tar.gz
Windows Binary IsoformSwitchAnalyzeR_1.7.1.zip
Mac OS X 10.11 (El Capitan) IsoformSwitchAnalyzeR_1.7.1.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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