recipe bioconductor-iggeneusage

Differential gene usage in immune repertoires

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-iggeneusage/meta.yaml

Detection of biases in the usage of immunoglobulin (Ig) genes is an important task in immune repertoire profiling. IgGeneUsage detects aberrant Ig gene usage between biological conditions using a probabilistic model which is analyzed computationally by Bayes inference. With this IgGeneUsage also avoids some common problems related to the current practice of null-hypothesis significance testing.

package bioconductor-iggeneusage

versions:

1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.8.0-2,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-1, 

1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.8.0-2,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.1-0,  1.0.0-0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0a0

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-bh:

>=1.66.0

depends r-rcpp:

>=0.12.0

depends r-rcppeigen:

>=0.3.3.3.0

depends r-rcppparallel:

>=5.0.1

depends r-reshape2:

>=1.4.3

depends r-rstan:

>=2.18.1

depends r-rstantools:

>=2.2.0

depends r-stanheaders:

>=2.18.0

depends r-tidyr:

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-iggeneusage

and update with::

   mamba update bioconductor-iggeneusage

To create a new environment, run:

mamba create --name myenvname bioconductor-iggeneusage

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-iggeneusage:<tag>

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

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