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.
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("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 | ||
| 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 | 1.12.0 |
| 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 |
See More
| Suggests | knitr, BSgenome.Hsapiens.UCSC.hg19, cummeRbund |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | IsoformSwitchAnalyzeR_1.12.0.tar.gz |
| Windows Binary | IsoformSwitchAnalyzeR_1.12.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | IsoformSwitchAnalyzeR_1.12.0.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 3.12 | Source Archive |