VaSP

Quantification and Visualization of Variations of Splicing in Population

Bioconductor version: Release (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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AlternativeSplicing, Clustering, DifferentialExpression, DifferentialSplicing, ImmunoOncology, KEGG, Preprocessing, RNASeq, Software, StatisticalMethod, Visualization
Version	1.16.0
In Bioconductor since	BioC 3.12 (R-4.0) (4 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

Suggests	knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	VaSP_1.16.0.tar.gz
Windows Binary (x86_64)	VaSP_1.16.0.zip (64-bit only)
macOS Binary (x86_64)	VaSP_1.16.0.tgz
macOS Binary (arm64)	VaSP_1.16.0.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