IVAS

This is the development version of IVAS; for the stable release version, see IVAS.

Identification of genetic Variants affecting Alternative Splicing

Bioconductor version: Development (3.24)

Identification of genetic variants affecting alternative splicing.

Author: Seonggyun Han, Sangsoo Kim

Maintainer: Seonggyun Han <hangost at ssu.ac.kr>

Citation (from within R, enter citation("IVAS")):

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("IVAS")

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("IVAS")

IVAS : Identification of genetic Variants affecting Alternative Splicing	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, GeneRegulation, ImmunoOncology, RNASeq, Regression, SNP, Sequencing, Software, Transcription
Version	2.33.0
In Bioconductor since	BioC 3.1 (R-3.2) (11.5 years)
License	GPL-2
Depends	R (> 3.0.0), GenomicFeatures, ggplot2, Biobase
Imports	doParallel, lme4, BiocGenerics, GenomicRanges, IRanges, foreach, AnnotationDbi, S4Vectors, Seqinfo, ggfortify, grDevices, methods, Matrix, BiocParallel, utils, stats
System Requirements
URL

Suggests	BiocStyle
Linking To
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Depends On Me
Imports Me
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Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	IVAS_2.33.0.tar.gz
Windows Binary (x86_64)	IVAS_2.33.0.zip
macOS Binary (big-sur-x86_64)	IVAS_2.33.0.tgz
macOS Binary (sonoma-arm64)	IVAS_2.33.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/IVAS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/IVAS
Bioc Package Browser	https://code.bioconductor.org/browse/IVAS/
Package Short Url	https://bioconductor.org/packages/IVAS/
Package Downloads Report	Download Stats