recipe bioconductor-hibag

HLA Genotype Imputation with Attribute Bagging

Homepage:

https://bioconductor.org/packages/3.20/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

(downloads) docker_bioconductor-hibag

Versions:
1.46.0-0,  1.42.0-1,  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, 

1.46.0-0,  1.42.0-1,  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:

  • on libblas >=3.9.0,<4.0a0

  • on libgcc >=14

  • on liblapack >=3.9.0,<4.0a0

  • on liblzma >=5.8.2,<6.0a0

  • on libstdcxx >=14

  • on libzlib >=1.3.1,<2.0a0

  • on r-base >=4.5,<4.6.0a0

  • on r-rcppparallel >=5.0.0

  • on tbb-devel >=2022.3.0,<2022.4.0a0

Additional platforms:
linux-aarch64

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-hibag

to add into an existing workspace instead, run:

pixi add bioconductor-hibag

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-hibag

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-hibag

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-hibag:<tag>

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

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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