Package Recipe 'bioconductor-microbiomeexplorer'

recipe bioconductor-microbiomeexplorer

Microbiome Exploration App

Homepage:: https://bioconductor.org/packages/3.18/bioc/html/microbiomeExplorer.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-microbiomeexplorer/meta.yaml

The MicrobiomeExplorer R package is designed to facilitate the analysis and visualization of marker-gene survey feature data. It allows a user to perform and visualize typical microbiome analytical workflows either through the command line or an interactive Shiny application included with the package. In addition to applying common analytical workflows the application enables automated analysis report generation.

package bioconductor-microbiomeexplorer¶

Versions:

1.20.0-0, 1.12.0-0, 1.10.0-0, 1.8.0-0, 1.4.0-0, 1.2.0-0, 1.0.1-1, 1.0.1-0

Depends:

on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-biomformat >=1.38.0,<1.39.0
on bioconductor-deseq2 >=1.50.0,<1.51.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-metagenomeseq >=1.52.0,<1.53.0
on r-base >=4.5,<4.6.0a0
on r-broom
on r-car
on r-dplyr
on r-dt >=0.12.0
on r-forcats
on r-heatmaply
on r-knitr
on r-lubridate
on r-magrittr
on r-matrixstats
on r-plotly >=4.9.1
on r-purrr
on r-rcolorbrewer
on r-readr
on r-reshape2
on r-rlang
on r-rmarkdown >=1.9.0
on r-shiny
on r-shinycssloaders
on r-shinydashboard
on r-shinyjs >=2.0.0
on r-shinywidgets
on r-stringr
on r-tibble
on r-tidyr
on r-vegan

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-microbiomeexplorer

to add into an existing workspace instead, run:

pixi add bioconductor-microbiomeexplorer

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-microbiomeexplorer

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-microbiomeexplorer

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-microbiomeexplorer:<tag>

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