VaSP

DOI: 10.18129/B9.bioc.VaSP    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see VaSP.

Quantification and Visualization of Variations of Splicing in Population

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

HTML	R Script	user guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	AlternativeSplicing, Clustering, DifferentialExpression, DifferentialSplicing, ImmunoOncology, KEGG, Preprocessing, RNASeq, Software, StatisticalMethod, Visualization
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2 years)
License	GPL (>= 2.0)
Depends	R (>= 4.0), ballgown
Imports	IRanges, GenomicRanges, S4Vectors, parallel, matrixStats, GenomicAlignments, GenomeInfoDb, Rsamtools, cluster, stats, graphics, methods
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/yuhuihui2011/VaSP
BugReports	https://github.com/yuhuihui2011/VaSP/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	VaSP_1.8.0.tar.gz
Windows Binary	VaSP_1.8.0.zip (64-bit only)
macOS Binary (x86_64)	VaSP_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/VaSP
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/VaSP
Package Short Url	https://bioconductor.org/packages/VaSP/
Package Downloads Report	Download Stats