recipe bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38

Extra SNP locations for Homo sapiens (dbSNP Build 144)

Homepage:

https://bioconductor.org/packages/3.17/data/annotation/html/XtraSNPlocs.Hsapiens.dbSNP144.GRCh38.html

License:

Artistic-2.0

Recipe:

/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/meta.yaml

Extra SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 30, 2015, and contain SNPs mapped to reference genome GRCh38.p2 (a patched version of GRCh38 that doesn't alter chromosomes 1-22, X, Y, MT). While the SNPlocs.Hsapiens.dbSNP144.GRCh38 package contains only molecular variations of class "snp", this package contains molecular variations of other classes (in-del, heterozygous, microsatellite, named-locus, no-variation, mixed, and multinucleotide-polymorphism).

package bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38

(downloads) docker_bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38

versions:
0.99.12-12,  0.99.12-11,  0.99.12-10,  0.99.12-9,  0.99.12-8,  0.99.12-7,  0.99.12-6,  0.99.12-5,  0.99.12-4, 

0.99.12-12,  0.99.12-11,  0.99.12-10,  0.99.12-9,  0.99.12-8,  0.99.12-7,  0.99.12-6,  0.99.12-5,  0.99.12-4,  0.99.12-3,  0.99.12-0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-bsgenome:

>=1.68.0,<1.69.0

depends bioconductor-data-packages:

>=20230706

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends curl:

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-xtrasnplocs.hsapiens.dbsnp144.grch38

and update with::

   mamba update bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38

To create a new environment, run:

mamba create --name myenvname bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38

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-xtrasnplocs.hsapiens.dbsnp144.grch38:<tag>

(see `bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/tags`_ for valid values for ``<tag>``)

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