recipe bioconductor-scoreinvhap

Get inversion status in predefined regions

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/scoreInvHap.html

License:

file LICENSE

Recipe:

/bioconductor-scoreinvhap/meta.yaml

scoreInvHap can get the samples' inversion status of known inversions. scoreInvHap uses SNP data as input and requires the following information about the inversion: genotype frequencies in the different haplotypes, R2 between the region SNPs and inversion status and heterozygote genotypes in the reference. The package include this data for 21 inversions.

package bioconductor-scoreinvhap

versions:

1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.1-0,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1, 

1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.1-0,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.4.0-0

depends bioconductor-biocparallel:

>=1.34.0,<1.35.0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-snpstats:

>=1.50.0,<1.51.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends bioconductor-variantannotation:

>=1.46.0,<1.47.0

depends r-base:

>=4.3,<4.4.0a0

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-scoreinvhap

and update with::

   mamba update bioconductor-scoreinvhap

To create a new environment, run:

mamba create --name myenvname bioconductor-scoreinvhap

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-scoreinvhap:<tag>

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

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