Bioconductor version: Release (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")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("IsoformSwitchAnalyzeR")
HTML | R Script | IsoformSwitchAnalyzeR |
Reference Manual | ||
Text | NEWS |
biocViews | AlternativeSplicing, Annotation, BiomedicalInformatics, DataImport, DifferentialExpression, DifferentialSplicing, FunctionalGenomics, FunctionalPrediction, GeneExpression, GenePrediction, MultipleComparison, RNASeq, Sequencing, Software, StatisticalMethod, SystemsBiology, Transcription, TranscriptomeVariant, Transcriptomics, Visualization |
Version | 1.0.0 |
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 |
LinkingTo | |
Suggests | knitr, BSgenome.Hsapiens.UCSC.hg19 |
SystemRequirements | |
Enhances | |
URL | http://bioconductor.org/packages/IsoformSwitchAnalyzeR/ |
BugReports | https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | IsoformSwitchAnalyzeR_1.0.0.tar.gz |
Windows Binary | IsoformSwitchAnalyzeR_1.0.0.zip |
Mac OS X 10.11 (El Capitan) | IsoformSwitchAnalyzeR_1.0.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/IsoformSwitchAnalyzeR |
Package Short Url | http://bioconductor.org/packages/IsoformSwitchAnalyzeR/ |
Package Downloads Report | Download Stats |
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