recipe bioconductor-twilight

Estimation of local false discovery rate

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/twilight.html

License:

GPL (>= 2)

Recipe:

/bioconductor-twilight/meta.yaml

Links:

biotools: twilight, doi: 10.1093/bioinformatics/bti436

In a typical microarray setting with gene expression data observed under two conditions, the local false discovery rate describes the probability that a gene is not differentially expressed between the two conditions given its corrresponding observed score or p-value level. The resulting curve of p-values versus local false discovery rate offers an insight into the twilight zone between clear differential and clear non-differential gene expression. Package 'twilight' contains two main functions: Function twilight.pval performs a two-condition test on differences in means for a given input matrix or expression set and computes permutation based p-values. Function twilight performs a stochastic downhill search to estimate local false discovery rates and effect size distributions. The package further provides means to filter for permutations that describe the null distribution correctly. Using filtered permutations, the influence of hidden confounders could be diminished.

package bioconductor-twilight

(downloads) docker_bioconductor-twilight

versions:
1.78.0-0,  1.76.0-0,  1.74.0-1,  1.74.0-0,  1.70.0-2,  1.70.0-1,  1.70.0-0,  1.68.0-0,  1.66.0-1, 

1.78.0-0,  1.76.0-0,  1.74.0-1,  1.74.0-0,  1.70.0-2,  1.70.0-1,  1.70.0-0,  1.68.0-0,  1.66.0-1,  1.66.0-0,  1.64.0-0,  1.62.0-0,  1.60.0-1,  1.58.0-1,  1.58.0-0,  1.56.0-0,  1.54.0-0,  1.52.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.3,<4.4.0a0

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-twilight

and update with::

   mamba update bioconductor-twilight

To create a new environment, run:

mamba create --name myenvname bioconductor-twilight

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-twilight:<tag>

(see `bioconductor-twilight/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

Render an install-with-bioconda 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-twilight/README.html)