Package Recipe 'bioconductor-nethet'

recipe bioconductor-nethet

A bioconductor package for high-dimensional exploration of biological network heterogeneity

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/nethet.html
License:: GPL-2
Recipe:: /bioconductor-nethet/meta.yaml

Package nethet is an implementation of statistical solid methodology enabling the analysis of network heterogeneity from high-dimensional data. It combines several implementations of recent statistical innovations useful for estimation and comparison of networks in a heterogeneous, high-dimensional setting. In particular, we provide code for formal two-sample testing in Gaussian graphical models (differential network and GGM-GSA; Stadler and Mukherjee, 2013, 2014) and make a novel network-based clustering algorithm available (mixed graphical lasso, Stadler and Mukherjee, 2013).

package bioconductor-nethet¶

Versions:

1.42.0-0, 1.38.0-0, 1.34.0-0, 1.32.0-0, 1.30.0-1, 1.30.0-0, 1.26.0-2, 1.26.0-1, 1.26.0-0,

1.42.0-0, 1.38.0-0, 1.34.0-0, 1.32.0-0, 1.30.0-1, 1.30.0-0, 1.26.0-2, 1.26.0-1, 1.26.0-0, 1.24.0-0, 1.22.0-1, 1.22.0-0, 1.20.0-0, 1.18.0-0, 1.16.1-0, 1.14.0-0

Depends:

on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-limma >=3.66.0,<3.67.0a0
on bioconductor-multtest >=2.66.0,<2.67.0
on bioconductor-multtest >=2.66.0,<2.67.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-compquadform
on r-genenet
on r-ggm
on r-ggplot2
on r-glasso
on r-glmnet
on r-gsa
on r-huge
on r-icsnp
on r-mclust
on r-mvtnorm
on r-network

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-nethet

to add into an existing workspace instead, run:

pixi add bioconductor-nethet

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-nethet

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-nethet

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-nethet:<tag>

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