recipe bioconductor-hibag

HLA Genotype Imputation with Attribute Bagging

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-hibag/meta.yaml

Links:

biotools: hibag

Imputes HLA classical alleles using GWAS SNP data, and it relies on a training set of HLA and SNP genotypes. HIBAG can be used by researchers with published parameter estimates instead of requiring access to large training sample datasets. It combines the concepts of attribute bagging, an ensemble classifier method, with haplotype inference for SNPs and HLA types. Attribute bagging is a technique which improves the accuracy and stability of classifier ensembles using bootstrap aggregating and random variable selection.

package bioconductor-hibag

versions:

1.42.0-0,  1.38.0-1,  1.38.0-0,  1.36.0-0,  1.34.0-1,  1.34.0-0,  1.30.2-1,  1.30.2-0,  1.30.0-0, 

1.42.0-0,  1.38.0-1,  1.38.0-0,  1.36.0-0,  1.34.0-1,  1.34.0-0,  1.30.2-1,  1.30.2-0,  1.30.0-0,  1.28.0-0,  1.26.1-0,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.18.1-0,  1.16.0-0,  1.14.0-0

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-rcppparallel:

>=5.0.0

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-hibag

and update with::

   mamba update bioconductor-hibag

To create a new environment, run:

mamba create --name myenvname bioconductor-hibag

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-hibag:<tag>

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

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