Package Recipe 'bioconductor-qrscore'

recipe bioconductor-qrscore

Quantile Rank Score

Homepage:: https://bioconductor.org/packages/3.22/bioc/html/QRscore.html
License:: GPL (>= 3)
Recipe:: /bioconductor-qrscore/meta.yaml

In genomics, differential analysis enables the discovery of groups of genes implicating important biological processes such as cell differentiation and aging. Non-parametric tests of differential gene expression usually detect shifts in centrality (such as mean or median), and therefore suffer from diminished power against alternative hypotheses characterized by shifts in spread (such as variance). This package provides a flexible family of non-parametric two-sample tests and K-sample tests, which is based on theoretical work around non-parametric tests, spacing statistics and local asymptotic normality (Erdmann-Pham et al., 2022+ [arXiv:2008.06664v2]; Erdmann-Pham, 2023+ [arXiv:2209.14235v2]).

package bioconductor-qrscore¶

Versions:

1.2.0-0

Depends:

on bioconductor-biocparallel >=1.44.0,<1.45.0
on r-arrangements
on r-assertthat
on r-base >=4.5,<4.6.0a0
on r-dplyr
on r-hitandrun
on r-mass
on r-pscl

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-qrscore

to add into an existing workspace instead, run:

pixi add bioconductor-qrscore

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-qrscore

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-qrscore

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-qrscore:<tag>

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