SCANVIS

DOI: 10.18129/B9.bioc.SCANVIS    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see SCANVIS.

SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions

Bioconductor version: 3.11

SCANVIS is a set of annotation-dependent tools for analyzing splice junctions and their read support as predetermined by an alignment tool of choice (for example, STAR aligner). SCANVIS assesses each junction's relative read support (RRS) by relating to the context of local split reads aligning to annotated transcripts. SCANVIS also annotates each splice junction by indicating whether the junction is supported by annotation or not, and if not, what type of junction it is (e.g. exon skipping, alternative 5' or 3' events, Novel Exons). Unannotated junctions are also futher annotated by indicating whether it induces a frame shift or not. SCANVIS includes a visualization function to generate static sashimi-style plots depicting relative read support and number of split reads using arc thickness and arc heights, making it easy for users to spot well-supported junctions. These plots also clearly delineate unannotated junctions from annotated ones using designated color schemes, and users can also highlight splice junctions of choice. Variants and/or a read profile are also incoroporated into the plot if the user supplies variants in bed format and/or the BAM file. One further feature of the visualization function is that users can submit multiple samples of a certain disease or cohort to generate a single plot - this occurs via a "merge" function wherein junction details over multiple samples are merged to generate a single sashimi plot, which is useful when contrasting cohorots (eg. disease vs control).

Author: Phaedra Agius <pagius at nygenome.org>

Maintainer: Phaedra Agius <pagius at nygenome.org>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("SCANVIS")

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("SCANVIS")

 

PDF	R Script	SCANVIS
PDF		Reference Manual
Text		LICENSE

Details

biocViews	Annotation, ResearchField, Software, Transcriptomics, Visualization, WorkflowStep
Version	1.2.0
In Bioconductor since	BioC 3.10 (R-3.6) (1 year)
License	file LICENSE
Depends	R (>= 3.6)
Imports	IRanges, plotrix, RCurl, rtracklayer
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
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	SCANVIS_1.2.0.tar.gz
Windows Binary	SCANVIS_1.2.0.zip
macOS 10.13 (High Sierra)	SCANVIS_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SCANVIS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SCANVIS
Package Short Url	https://bioconductor.org/packages/SCANVIS/
Package Downloads Report	Download Stats