Package Recipe 'bioconductor-phenomis'

recipe bioconductor-phenomis

Postprocessing and univariate analysis of omics data

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/phenomis.html
License:: CeCILL
Recipe:: /bioconductor-phenomis/meta.yaml

The 'phenomis' package provides methods to perform post-processing (i.e. quality control and normalization) as well as univariate statistical analysis of single and multi-omics data sets. These methods include quality control metrics, signal drift and batch effect correction, intensity transformation, univariate hypothesis testing, but also clustering (as well as annotation of metabolomics data). The data are handled in the standard Bioconductor formats (i.e. SummarizedExperiment and MultiAssayExperiment for single and multi-omics datasets, respectively; the alternative ExpressionSet and MultiDataSet formats are also supported for convenience). As a result, all methods can be readily chained as workflows. The pipeline can be further enriched by multivariate analysis and feature selection, by using the 'ropls' and 'biosigner' packages, which support the same formats. Data can be conveniently imported from and exported to text files. Although the methods were initially targeted to metabolomics data, most of the methods can be applied to other types of omics data (e.g., transcriptomics, proteomics).

package bioconductor-phenomis¶

Versions:

1.12.0-0, 1.8.0-0, 1.4.0-0, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-biodb >=1.18.0,<1.19.0
on bioconductor-biodbchebi >=1.16.0,<1.17.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-multiassayexperiment >=1.36.0,<1.37.0
on bioconductor-multidataset >=1.38.0,<1.39.0
on bioconductor-ropls >=1.42.0,<1.43.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-futile.logger
on r-ggplot2
on r-ggrepel
on r-htmlwidgets
on r-igraph
on r-plotly
on r-pmcmrplus
on r-ranger
on r-rcolorbrewer
on r-tibble
on r-tidyr
on r-venndiagram

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-phenomis

to add into an existing workspace instead, run:

pixi add bioconductor-phenomis

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-phenomis

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-phenomis

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-phenomis:<tag>

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