recipe bioconductor-normalyzerde

Evaluation of normalization methods and calculation of differential expression analysis statistics

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-normalyzerde/meta.yaml

NormalyzerDE provides screening of normalization methods for LC-MS based expression data. It calculates a range of normalized matrices using both existing approaches and a novel time-segmented approach, calculates performance measures and generates an evaluation report. Furthermore, it provides an easy utility for Limma- or ANOVA- based differential expression analysis.

package bioconductor-normalyzerde

versions:

1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0, 

1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.0.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-preprocesscore:

>=1.64.0,<1.65.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-vsn:

>=3.70.0,<3.71.0

depends r-ape:

depends r-base:

>=4.3,<4.4.0a0

depends r-car:

depends r-ggforce:

depends r-ggplot2:

depends r-mass:

depends r-matrixstats:

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-normalyzerde

and update with::

   mamba update bioconductor-normalyzerde

To create a new environment, run:

mamba create --name myenvname bioconductor-normalyzerde

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-normalyzerde:<tag>

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

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-normalyzerde/README.html)