recipe bioconductor-metaphor

Metabolic Pathway Analysis of RNA

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/MetaPhOR.html

License:

Artistic-2.0

Recipe:

/bioconductor-metaphor/meta.yaml

MetaPhOR was developed to enable users to assess metabolic dysregulation using transcriptomic-level data (RNA-sequencing and Microarray data) and produce publication-quality figures. A list of differentially expressed genes (DEGs), which includes fold change and p value, from DESeq2 or limma, can be used as input, with sample size for MetaPhOR, and will produce a data frame of scores for each KEGG pathway. These scores represent the magnitude and direction of transcriptional change within the pathway, along with estimated p-values.MetaPhOR then uses these scores to visualize metabolic profiles within and between samples through a variety of mechanisms, including: bubble plots, heatmaps, and pathway models.

package bioconductor-metaphor

(downloads) docker_bioconductor-metaphor

versions:

1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-clusterprofiler:

>=4.10.0,<4.11.0

depends bioconductor-rcy3:

>=2.22.0,<2.23.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-ggrepel:

depends r-pheatmap:

depends r-recordlinkage:

depends r-stringr:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-metaphor

and update with::

   mamba update bioconductor-metaphor

To create a new environment, run:

mamba create --name myenvname bioconductor-metaphor

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

(see `bioconductor-metaphor/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

Render an install-with-bioconda 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-metaphor/README.html)