IsoformSwitchAnalyzeR

This package is for version 3.12 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.

DOI: 10.18129/B9.bioc.IsoformSwitchAnalyzeR

Bioconductor version: 3.12

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 "4.0") 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

Need some help? Ask on the Bioconductor Support site!

Details

Version 1.12.0

In Bioconductor since BioC 3.6 (R-3.4) (6.5 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), tximeta(>= 1.7.12), edgeR, futile.logger, stringr, dplyr, magrittr, readr, tibble, XVector, BiocGenerics, RCurl

System Requirements

URL http://bioconductor.org/packages/IsoformSwitchAnalyzeR/

Bug Reports https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues

Suggests knitr, BSgenome.Hsapiens.UCSC.hg19, cummeRbund

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