recipe bioconductor-degnorm

DegNorm: degradation normalization for RNA-seq data

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/DegNorm.html

License:

LGPL (>= 3)

Recipe:

/bioconductor-degnorm/meta.yaml

This package performs degradation normalization in bulk RNA-seq data to improve differential expression analysis accuracy.

package bioconductor-degnorm

versions:

1.16.0-0,  1.12.0-0,  1.10.1-0,  1.8.0-1,  1.8.0-0,  1.4.0-2,  1.4.0-1,  1.4.0-0,  1.2.0-0, 

1.16.0-0,  1.12.0-0,  1.10.1-0,  1.8.0-1,  1.8.0-0,  1.4.0-2,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-2,  1.0.0-1

depends bioconductor-genomicalignments:

>=1.42.0,<1.43.0

depends bioconductor-genomicalignments:

>=1.42.0,<1.43.0a0

depends bioconductor-genomicfeatures:

>=1.58.0,<1.59.0

depends bioconductor-genomicfeatures:

>=1.58.0,<1.59.0a0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0a0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0a0

depends bioconductor-rsamtools:

>=2.22.0,<2.23.0

depends bioconductor-rsamtools:

>=2.22.0,<2.23.0a0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0a0

depends bioconductor-txdbmaker:

>=1.2.0,<1.3.0

depends bioconductor-txdbmaker:

>=1.2.0,<1.3.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

depends r-data.table:

depends r-doparallel:

depends r-foreach:

depends r-ggplot2:

depends r-heatmaply:

depends r-plotly:

depends r-plyr:

depends r-rcpp:

>=1.0.2

depends r-rcpparmadillo:

depends r-viridis:

requirements:

additional platforms:

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-degnorm

and update with::

   mamba update bioconductor-degnorm

To create a new environment, run:

mamba create --name myenvname bioconductor-degnorm

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-degnorm:<tag>

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

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Link to this page

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-degnorm/README.html)