recipe bioconductor-omicplotr

Visual Exploration of Omic Datasets Using a Shiny App

Homepage:

https://bioconductor.org/packages/3.16/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:

1.18.0-0,  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:

• bioconductor-aldex2 >=1.30.0,<1.31.0

• r-base >=4.2,<4.3.0a0

• r-compositions

• r-dt

• r-jsonlite

• r-knitr

• r-matrixstats

• r-rmarkdown

• r-shiny

• r-vegan

• r-zcompositions

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-omicplotr

and update with:

conda update bioconductor-omicplotr

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-omicplotr:<tag>

(see bioconductor-omicplotr/tags for valid values for <tag>)

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)