recipe vsclust

Interactive tool for statistical testing, data browsing and interactive visualization of quantitative omics data

Homepage:

https://bitbucket.org/veitveit/vsclust/src/master/

License:

GPL / GPL (>=2)

Recipe:

/vsclust/meta.yaml

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

(downloads) docker_vsclust

versions:

0.91-0,  0.87-0

depends bioconductor-clusterprofiler:

4.2.0.*

depends bioconductor-limma:

depends bioconductor-mfuzz:

depends bioconductor-qvalue:

depends r-base:

>=4.1,<4.2.0a0

depends r-data.table:

depends r-matrixstats:

depends r-parallelly:

depends r-readxl:

depends r-shinyjs:

depends r-shinythemes:

depends r-yaml:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install vsclust

and update with::

   mamba update vsclust

To create a new environment, run:

mamba create --name myenvname vsclust

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/vsclust:<tag>

(see `vsclust/tags`_ for valid values for ``<tag>``)

Notes

The shiny app can be run with the run_app.sh command. Alternative, a command-line version is available: runVSClust.R

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Link to this page

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