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VaSP

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

Quantification and Visualization of Variations of Splicing in Population


Bioconductor version: Development (3.19)

Discovery of genome-wide variable alternative splicing events from short-read RNA-seq data and visualizations of gene splicing information for publication-quality multi-panel figures in a population. (Warning: The visualizing function is removed due to the dependent package Sushi deprecated. If you want to use it, please change back to an older version.)

Author: Huihui Yu [aut, cre] , Qian Du [aut] , Chi Zhang [aut]

Maintainer: Huihui Yu <yuhuihui2011 at foxmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("VaSP")

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("VaSP")
user guide HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews AlternativeSplicing, Clustering, DifferentialExpression, DifferentialSplicing, ImmunoOncology, KEGG, Preprocessing, RNASeq, Software, StatisticalMethod, Visualization
Version 1.15.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL (>= 2.0)
Depends R (>= 4.0), ballgown
Imports IRanges, GenomicRanges, S4Vectors, parallel, matrixStats, GenomicAlignments, GenomeInfoDb, Rsamtools, cluster, stats, graphics, methods
System Requirements
URL https://github.com/yuhuihui2011/VaSP
Bug Reports https://github.com/yuhuihui2011/VaSP/issues
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Suggests knitr, rmarkdown
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Package Archives

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

Source Package VaSP_1.15.0.tar.gz
Windows Binary VaSP_1.15.0.zip
macOS Binary (x86_64) VaSP_1.15.0.tgz
macOS Binary (arm64) VaSP_1.15.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/VaSP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/VaSP
Bioc Package Browser https://code.bioconductor.org/browse/VaSP/
Package Short Url https://bioconductor.org/packages/VaSP/
Package Downloads Report Download Stats