Package: SCANVIS
Type: Package
Title: SCANVIS - a tool for SCoring, ANnotating and VISualizing splice
        junctions
Version: 1.24.0
Date: 2019-07-11
Author: Phaedra Agius <pagius@nygenome.org>
Maintainer: Phaedra Agius <pagius@nygenome.org>
Depends: R (>= 3.6)
Description: 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).
Imports: IRanges,plotrix,RCurl,rtracklayer
License: file LICENSE
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
biocViews:
        Software,ResearchField,Transcriptomics,WorkflowStep,Annotation,Visualization
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:53:09 UTC
RemoteUrl: https://github.com/bioc/SCANVIS
RemoteRef: RELEASE_3_22
RemoteSha: 5b11f6c12bb6a5a172406d29e233e7fe837d177c
NeedsCompilation: no
Packaged: 2026-02-01 09:28:10 UTC; root
Built: R 4.5.2; ; 2026-02-01 09:30:11 UTC; windows
