Package Recipe 'bioconductor-panomir'

recipe bioconductor-panomir

Detection of miRNAs that regulate interacting groups of pathways

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

PanomiR is a package to detect miRNAs that target groups of pathways from gene expression data. This package provides functionality for generating pathway activity profiles, determining differentially activated pathways between user-specified conditions, determining clusters of pathways via the PCxN package, and generating miRNAs targeting clusters of pathways. These function can be used separately or sequentially to analyze RNA-Seq data.

package bioconductor-panomir¶

Versions:

1.14.0-0, 1.10.0-0, 1.6.0-0, 1.4.0-0, 1.2.0-0

Depends:

on bioconductor-clusterprofiler >=4.18.0,<4.19.0
on bioconductor-gseabase >=1.72.0,<1.73.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-org.hs.eg.db >=3.22.0,<3.23.0
on bioconductor-preprocesscore >=1.72.0,<1.73.0
on r-base >=4.5,<4.6.0a0
on r-dplyr
on r-forcats
on r-igraph
on r-metap
on r-rcolorbrewer
on r-rlang
on r-tibble
on r-withr

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-panomir

to add into an existing workspace instead, run:

pixi add bioconductor-panomir

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-panomir

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-panomir

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-panomir:<tag>

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