Package Recipe 'bioconductor-omicplotr'

recipe bioconductor-omicplotr

Visual Exploration of Omic Datasets Using a Shiny App

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/omicplotR.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-omicplotr/meta.yaml

A Shiny app for visual exploration of omic datasets as compositions, and differential abundance analysis using ALDEx2. Useful for exploring RNA-seq, meta-RNA-seq, 16s rRNA gene sequencing with visualizations such as principal component analysis biplots (coloured using metadata for visualizing each variable), dendrograms and stacked bar plots, and effect plots (ALDEx2). Input is a table of counts and metadata file (if metadata exists), with options to filter data by count or by metadata to remove low counts, or to visualize select samples according to selected metadata.

package bioconductor-omicplotr¶

Versions:

1.30.0-0, 1.26.0-0, 1.22.0-0, 1.20.0-0, 1.18.0-0, 1.14.0-0, 1.12.0-0, 1.10.0-1, 1.10.0-0,

1.30.0-0, 1.26.0-0, 1.22.0-0, 1.20.0-0, 1.18.0-0, 1.14.0-0, 1.12.0-0, 1.10.0-1, 1.10.0-0, 1.8.0-0, 1.6.0-0, 1.4.0-1, 1.2.0-0

Depends:

on bioconductor-aldex2 >=1.42.0,<1.43.0
on r-base >=4.5,<4.6.0a0
on r-compositions
on r-dt
on r-jsonlite
on r-knitr
on r-matrixstats
on r-rmarkdown
on r-shiny
on r-vegan
on r-zcompositions

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-omicplotr

to add into an existing workspace instead, run:

pixi add bioconductor-omicplotr

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-omicplotr

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-omicplotr

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-omicplotr:<tag>

(see bioconductor-omicplotr/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-omicplotr/README.html)