- recipe bioconductor-scanvis
SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/SCANVIS.html
- License:
file LICENSE
- Recipe:
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).
- package bioconductor-scanvis¶
- Versions:
1.24.0-0,1.20.0-0,1.16.0-0,1.14.0-0,1.12.0-0,1.7.0-0,1.6.0-0,1.4.0-1,1.4.0-0,1.24.0-0,1.20.0-0,1.16.0-0,1.14.0-0,1.12.0-0,1.7.0-0,1.6.0-0,1.4.0-1,1.4.0-0,1.2.0-0,1.0.0-0- Depends:
on bioconductor-iranges
>=2.44.0,<2.45.0on bioconductor-rtracklayer
>=1.70.0,<1.71.0on r-base
>=4.5,<4.6.0a0on r-plotrix
on r-rcurl
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install bioconductor-scanvis
to add into an existing workspace instead, run:
pixi add bioconductor-scanvis
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install bioconductor-scanvis
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-scanvis
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/bioconductor-scanvis:<tag>
(see bioconductor-scanvis/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-scanvis/README.html)
