recipe bioconductor-lpeadj

A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size.

Homepage:

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

License:

LGPL

Recipe:

/bioconductor-lpeadj/meta.yaml

Links:

biotools: lpeadj, doi: 10.1038/nmeth.3252

Two options are added to the LPE algorithm. The original LPE method sets all variances below the max variance in the ordered distribution of variances to the maximum variance. in LPEadj this option is turned off by default. The second option is to use a variance adjustment based on sample size rather than pi/2. By default the LPEadj uses the sample size based variance adjustment.

package bioconductor-lpeadj

(downloads) docker_bioconductor-lpeadj

versions:
1.62.0-0,  1.60.0-0,  1.58.0-0,  1.54.0-0,  1.52.0-0,  1.50.0-1,  1.50.0-0,  1.48.0-0,  1.46.0-0, 

1.62.0-0,  1.60.0-0,  1.58.0-0,  1.54.0-0,  1.52.0-0,  1.50.0-1,  1.50.0-0,  1.48.0-0,  1.46.0-0,  1.44.0-1,  1.44.0-0,  1.42.0-0,  1.40.0-0,  1.38.0-0

depends bioconductor-lpe:

>=1.76.0,<1.77.0

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-lpeadj

and update with::

   mamba update bioconductor-lpeadj

To create a new environment, run:

mamba create --name myenvname bioconductor-lpeadj

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-lpeadj:<tag>

(see `bioconductor-lpeadj/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-lpeadj/README.html)