recipe bioconductor-scbn

A statistical normalization method and differential expression analysis for RNA-seq data between different species

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-scbn/meta.yaml

This package provides a scale based normalization (SCBN) method to identify genes with differential expression between different species. It takes into account the available knowledge of conserved orthologous genes and the hypothesis testing framework to detect differentially expressed orthologous genes. The method on this package are described in the article 'A statistical normalization method and differential expression analysis for RNA-seq data between different species' by Yan Zhou, Jiadi Zhu, Tiejun Tong, Junhui Wang, Bingqing Lin, Jun Zhang (2018, pending publication).

package bioconductor-scbn

(downloads) docker_bioconductor-scbn

versions:
1.20.0-1,  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, 

1.20.0-1,  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,  1.2.0-0,  1.0.0-0

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-scbn

and update with::

   mamba update bioconductor-scbn

To create a new environment, run:

mamba create --name myenvname bioconductor-scbn

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-scbn:<tag>

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