|
|
|
|
|
|
Bioconductor version: Release (3.8)
IsoformSwitchAnalyzeR enables identification and analysis of alternative splicing and 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")
):
To install this package, start R (version "3.5") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("IsoformSwitchAnalyzeR", version = "3.8")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("IsoformSwitchAnalyzeR")
HTML | R Script | IsoformSwitchAnalyzeR |
Reference Manual | ||
Text | NEWS |
biocViews | AlternativeSplicing, Annotation, BatchEffect, BiomedicalInformatics, DataImport, DifferentialExpression, DifferentialSplicing, FunctionalGenomics, FunctionalPrediction, GeneExpression, GenePrediction, MultipleComparison, RNASeq, Software, StatisticalMethod, SystemsBiology, Transcription, TranscriptomeVariant, Transcriptomics, Visualization |
Version | 1.4.0 |
License | GPL (>= 2) |
Depends | R (>= 3.5), limma, DEXSeq, ggplot2 |
Imports | methods, BSgenome, plyr, reshape2, gridExtra, Biostrings, IRanges, GenomicRanges, DRIMSeq, RColorBrewer, rtracklayer, VennDiagram, DBI, grDevices, graphics, stats, utils, GenomeInfoDb, grid, tximport(>= 1.7.1), edgeR, futile.logger, limma, stringr, dplyr, magrittr, readr |
LinkingTo | |
Suggests | knitr, BSgenome.Hsapiens.UCSC.hg19, cummeRbund |
SystemRequirements | |
Enhances | |
URL | http://bioconductor.org/packages/IsoformSwitchAnalyzeR/ |
BugReports | https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | IsoformSwitchAnalyzeR_1.4.0.tar.gz |
Windows Binary | IsoformSwitchAnalyzeR_1.4.0.zip (32- & 64-bit) |
Mac OS X 10.11 (El Capitan) | IsoformSwitchAnalyzeR_1.4.0.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 | http://bioconductor.org/packages/IsoformSwitchAnalyzeR/ |
Package Downloads Report | Download Stats |
Documentation »
Bioconductor
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations: