recipe bioconductor-hapfabia

hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data

Homepage:

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

License:

LGPL (>= 2.1)

Recipe:

/bioconductor-hapfabia/meta.yaml

Links:

biotools: hapfabia

A package to identify very short IBD segments in large sequencing data by FABIA biclustering. Two haplotypes are identical by descent (IBD) if they share a segment that both inherited from a common ancestor. Current IBD methods reliably detect long IBD segments because many minor alleles in the segment are concordant between the two haplotypes. However, many cohort studies contain unrelated individuals which share only short IBD segments. This package provides software to identify short IBD segments in sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats.

package bioconductor-hapfabia

versions:

1.48.0-0,  1.44.0-0,  1.42.0-0,  1.40.0-1,  1.40.0-0,  1.36.0-2,  1.36.0-1,  1.36.0-0,  1.34.0-0, 

1.48.0-0,  1.44.0-0,  1.42.0-0,  1.40.0-1,  1.40.0-0,  1.36.0-2,  1.36.0-1,  1.36.0-0,  1.34.0-0,  1.32.0-1,  1.32.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-1,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0

depends bioconductor-biobase:

>=2.66.0,<2.67.0

depends bioconductor-biobase:

>=2.66.0,<2.67.0a0

depends bioconductor-fabia:

>=2.52.0,<2.53.0

depends bioconductor-fabia:

>=2.52.0,<2.53.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.4,<4.5.0a0

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-hapfabia

and update with::

   mamba update bioconductor-hapfabia

To create a new environment, run:

mamba create --name myenvname bioconductor-hapfabia

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-hapfabia:<tag>

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

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