Package Recipe 'bioconductor-chronos'

recipe bioconductor-chronos

CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/CHRONOS.html
License:: GPL-2
Recipe:: /bioconductor-chronos/meta.yaml
Links:: biotools: CHRONOS

A package used for efficient unraveling of the inherent dynamic properties of pathways. MicroRNA-mediated subpathway topologies are extracted and evaluated by exploiting the temporal transition and the fold change activity of the linked genes/microRNAs.

package bioconductor-chronos¶

Versions:

1.38.0-0, 1.34.0-0, 1.30.0-0, 1.28.0-0, 1.26.0-0, 1.22.0-0, 1.20.0-0, 1.18.0-1, 1.18.0-0,

1.38.0-0, 1.34.0-0, 1.30.0-0, 1.28.0-0, 1.26.0-0, 1.22.0-0, 1.20.0-0, 1.18.0-1, 1.18.0-0, 1.16.0-0, 1.14.0-0, 1.12.0-1, 1.10.0-0, 1.8.1-0, 1.6.0-0, 1.4.0-0

Depends:

on bioconductor-biomart >=2.66.0,<2.67.0
on bioconductor-graph >=1.88.0,<1.89.0
on bioconductor-rbgl >=1.86.0,<1.87.0
on openjdk
on r-base >=4.5,<4.6.0a0
on r-circlize
on r-doparallel
on r-foreach
on r-igraph
on r-openxlsx
on r-rcurl
on r-rjava
on r-xml

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-chronos

to add into an existing workspace instead, run:

pixi add bioconductor-chronos

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-chronos

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-chronos

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-chronos:<tag>

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