recipe bioconductor-nanostringdiff

Differential Expression Analysis of NanoString nCounter Data

Homepage:

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

License:

GPL

Recipe:

/bioconductor-nanostringdiff/meta.yaml

This Package utilizes a generalized linear model(GLM) of the negative binomial family to characterize count data and allows for multi-factor design. NanoStrongDiff incorporate size factors, calculated from positive controls and housekeeping controls, and background level, obtained from negative controls, in the model framework so that all the normalization information provided by NanoString nCounter Analyzer is fully utilized.

package bioconductor-nanostringdiff

versions:

1.32.0-0,  1.30.0-0,  1.28.0-1,  1.28.0-0,  1.24.0-2,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-1, 

1.32.0-0,  1.30.0-0,  1.28.0-1,  1.28.0-0,  1.24.0-2,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.12.0-0

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 libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-matrixstats:

depends r-rcpp:

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-nanostringdiff

and update with::

   mamba update bioconductor-nanostringdiff

To create a new environment, run:

mamba create --name myenvname bioconductor-nanostringdiff

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-nanostringdiff:<tag>

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

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