IsoformSwitchAnalyzeR

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see IsoformSwitchAnalyzeR.

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


Bioconductor version: 3.13

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, StringTie, Cufflinks/Cuffdiff etc.

Author: Kristoffer Vitting-Seerup [cre, aut]

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 "4.1") 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, BatchEffect, BiomedicalInformatics, DataImport, DifferentialExpression, DifferentialSplicing, FunctionalGenomics, FunctionalPrediction, GeneExpression, GenePrediction, ImmunoOncology, MultipleComparison, RNASeq, Software, StatisticalMethod, SystemsBiology, Transcription, TranscriptomeVariant, Transcriptomics, Visualization
Version 1.14.1
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL (>= 2)
Depends R (>= 3.6), 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, Biobase
System Requirements
URL http://bioconductor.org/packages/IsoformSwitchAnalyzeR/
Bug Reports https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues
See More
Suggests knitr, BSgenome.Hsapiens.UCSC.hg19, rmarkdown
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Package Archives

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

Source Package IsoformSwitchAnalyzeR_1.14.1.tar.gz
Windows Binary IsoformSwitchAnalyzeR_1.14.1.zip
macOS 10.13 (High Sierra) IsoformSwitchAnalyzeR_1.14.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/IsoformSwitchAnalyzeR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/IsoformSwitchAnalyzeR
Bioc Package Browser https://code.bioconductor.org/browse/IsoformSwitchAnalyzeR/
Package Short Url https://bioconductor.org/packages/IsoformSwitchAnalyzeR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.13 Source Archive