recipe bioconductor-omxplore

Vizualization tools for 'omics' datasets with R

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/omXplore.html

License:

Artistic-2.0

Recipe:

/bioconductor-omxplore/meta.yaml

This package contains a collection of functions (written as shiny modules) for the visualisation and the statistical analysis of omics data. These plots can be displayed individually or embedded in a global Shiny module. Additionaly, it is possible to integrate third party modules to the main interface of the package omXplore.

package bioconductor-omxplore

versions:

1.0.0-0

depends bioconductor-msnbase:

>=2.32.0,<2.33.0

depends bioconductor-multiassayexperiment:

>=1.32.0,<1.33.0

depends bioconductor-psmatch:

>=1.10.0,<1.11.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dendextend:

depends r-dplyr:

depends r-dt:

depends r-factoextra:

depends r-factominer:

depends r-gplots:

depends r-highcharter:

depends r-htmlwidgets:

depends r-rcolorbrewer:

depends r-shiny:

depends r-shinybs:

depends r-shinyjqui:

depends r-shinyjs:

depends r-tibble:

depends r-tidyr:

depends r-vioplot:

depends r-visnetwork:

requirements:

additional platforms:

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 bioconductor-omxplore

and update with::

   mamba update bioconductor-omxplore

To create a new environment, run:

mamba create --name myenvname bioconductor-omxplore

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/bioconductor-omxplore:<tag>

(see `bioconductor-omxplore/tags`_ for valid values for ``<tag>``)

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Link to this page

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