- recipe vsclust
Interactive tool for statistical testing, data browsing and interactive visualization of quantitative omics data
- Homepage:
- License:
GPL / GPL (>=2)
- Recipe:
- Links:
biotools: vsclust, doi: 10.1093/bioinformatics/bty224
VSClust is a web service (shiny app) and command-line tool for statistical testing, clustering and interactive visualization of quantitative omics data. Its variance-sensitive clustering algorithm improves identification of co-regulated features in noisy data with replicates
- package vsclust¶
- Versions:
0.91-0,0.87-0- Depends:
on bioconductor-clusterprofiler
4.2.0.*on bioconductor-limma
on bioconductor-mfuzz
on bioconductor-qvalue
on r-base
>=4.1,<4.2.0a0on r-data.table
on r-matrixstats
on r-parallelly
on r-readxl
on r-shinyjs
on r-shinythemes
on r-yaml
- 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 vsclust
to add into an existing workspace instead, run:
pixi add vsclust
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 vsclust
Alternatively, to install into a new environment, run:
conda create -n envname vsclust
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/vsclust:<tag>
(see vsclust/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.
Notes¶
The shiny app can be run with the run_app.sh command. Alternative, a command-line version is available: runVSClust.R
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/vsclust/README.html)
