Package Recipe 'bioconductor-regparallel'

recipe bioconductor-regparallel

Standard regression functions in R enabled for parallel processing over large data-frames

Homepage:: https://bioconductor.org/packages/3.20/data/experiment/html/RegParallel.html
License:: GPL-3
Recipe:: /bioconductor-regparallel/meta.yaml

In many analyses, a large amount of variables have to be tested independently against the trait/endpoint of interest, and also adjusted for covariates and confounding factors at the same time. The major bottleneck in these is the amount of time that it takes to complete these analyses. With RegParallel, a large number of tests can be performed simultaneously. On a 12-core system, 144 variables can be tested simultaneously, with 1000s of variables processed in a matter of seconds via 'nested' parallel processing. Works for logistic regression, linear regression, conditional logistic regression, Cox proportional hazards and survival models, and Bayesian logistic regression. Also caters for generalised linear models that utilise survey weights created by the 'survey' CRAN package and that utilise 'survey::svyglm'.

package bioconductor-regparallel¶

Versions:

1.28.0-0, 1.24.0-0, 1.20.0-0, 1.18.0-0, 1.15.0-0, 1.12.0-1, 1.12.0-0, 1.10.0-0, 1.8.0-1,

1.28.0-0, 1.24.0-0, 1.20.0-0, 1.18.0-0, 1.15.0-0, 1.12.0-1, 1.12.0-0, 1.10.0-0, 1.8.0-1, 1.8.0-0, 1.7.6-0, 1.6.0-0, 1.4.0-0, 1.2.0-1, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-data-packages >=20260207
on curl
on r-arm
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-doparallel
on r-foreach
on r-iterators
on r-stringr
on r-survival

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-regparallel

to add into an existing workspace instead, run:

pixi add bioconductor-regparallel

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-regparallel

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-regparallel

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-regparallel:<tag>

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