IVAS specifications

Information


Unique identifier OMICS_22564
Name IVAS
Alternative name Identification of genetic Variants affecting Alternative Splicing
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.0.0
Stability Stable
Requirements
AnnotationDbi, methods, stats, BiocGenerics, Biobase, IRanges, GenomicRanges, Matrix, utils, S4Vectors, GenomeInfoDb, BiocStyle, grDevices, ggplot2, BiocParallel, GenomicFeatures, foreach, doParallel, lme4, R(>3.0.0), ggfortify
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Seonggyun Han

IVAS citation

library_books

The effects of alternative splicing on miRNA binding sites in bladder cancer

2018
PLoS One
PMCID: 5754136
PMID: 29300757
DOI: 10.1371/journal.pone.0190708

[…] pt isoforms. For a specific exon t, that is an MBE in a 3′ UTR, the PSI value (denoted as a ratio between two groups of MBE-retaining and MBE-deleting mRNA isoforms t), Ψt, was estimated by using the identification of genetic variants affecting alternative splicing (IVAS), a Bioconductor package, which utilizes the following algorithm []: f(Ψt|3′UTR)=∑i=1n(Xit)(∑s=1n(Xst)+∑i=1n(Xit))Here, Xit and […]

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