Package Recipe 'bioconductor-omxplore'

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:

1.4.2-0, 1.0.0-0

Depends:

on bioconductor-msnbase >=2.36.0,<2.37.0
on bioconductor-multiassayexperiment >=1.36.0,<1.37.0
on bioconductor-psmatch >=1.14.0,<1.15.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-dendextend
on r-dplyr
on r-dt
on r-factoextra
on r-factominer
on r-gplots
on r-highcharter
on r-htmlwidgets
on r-nipals
on r-rcolorbrewer
on r-shiny
on r-shinybs
on r-shinyjqui
on r-shinyjs
on r-tibble
on r-tidyr
on r-vioplot
on r-visnetwork

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-omxplore

to add into an existing workspace instead, run:

pixi add bioconductor-omxplore

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-omxplore

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-omxplore

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-omxplore:<tag>

(see bioconductor-omxplore/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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-omxplore/README.html)