IsoformSwitchAnalyzeR

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see IsoformSwitchAnalyzeR.

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

DOI: 10.18129/B9.bioc.IsoformSwitchAnalyzeR

Bioconductor version: 3.6

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 (version "3.4") 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

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

Version 1.0.0

In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)

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

System Requirements

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

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

Suggests knitr, BSgenome.Hsapiens.UCSC.hg19

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report