IsoformSwitchAnalyzeR

DOI:10.18129/B9.bioc.IsoformSwitchAnalyzeR

This is thedevelopmentversion of IsoformSwitchAnalyzeR; for the stable release version, seeIsoformSwitchAnalyzeR.

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

Bioconductor version: Development (3.16)

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

Installation

To install this package, start R (version "4.2") and enter:

if (!require("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 appropriateBioconductor release.

Documentation

查看文档的版本包age installed in your system, start R and enter:

browseVignettes("IsoformSwitchAnalyzeR")

HTML	R Script	IsoformSwitchAnalyzeR
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	1.19.0
In Bioconductor since	BioC 3.6 (R-3.4) (4.5 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
LinkingTo
Suggests	knitr,BSgenome.Hsapiens.UCSC.hg19,rmarkdown
SystemRequirements
Enhances
URL	//www.andersvercelli.com/packages/IsoformSwitchAnalyzeR/
BugReports	https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow2021年欧洲杯比分预测 instructions to use this package in your R session.

Source Package	IsoformSwitchAnalyzeR_1.19.0.tar.gz
Windows Binary	IsoformSwitchAnalyzeR_1.19.0.zip
macOS 10.13 (High Sierra)	IsoformSwitchAnalyzeR_1.19.0.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	//www.andersvercelli.com/packages/IsoformSwitchAnalyzeR/
Package Downloads Report	Download Stats