recipe bioconductor-snplocs.hsapiens.dbsnp144.grch37

SNP locations for Homo sapiens (dbSNP Build 144)

Homepage:

https://bioconductor.org/packages/3.18/data/annotation/html/SNPlocs.Hsapiens.dbSNP144.GRCh37.html

License:

Artistic-2.0

Recipe:

/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml

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 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13. WARNING: Note that the GRCh37.p13 genome is a patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be "injected" in BSgenome.Hsapiens.UCSC.hg19 and they will land at the correct position but this injection will exclude chrM (i.e. nothing will be injected in that sequence).

package bioconductor-snplocs.hsapiens.dbsnp144.grch37

(downloads) docker_bioconductor-snplocs.hsapiens.dbsnp144.grch37

versions:
0.99.20-12,  0.99.20-11,  0.99.20-10,  0.99.20-9,  0.99.20-8,  0.99.20-7,  0.99.20-6,  0.99.20-5,  0.99.20-4, 

0.99.20-12,  0.99.20-11,  0.99.20-10,  0.99.20-9,  0.99.20-8,  0.99.20-7,  0.99.20-6,  0.99.20-5,  0.99.20-4,  0.99.20-3,  0.99.20-2,  0.99.20-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-bsgenome:

>=1.70.0,<1.71.0

depends bioconductor-data-packages:

>=20231203

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

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-snplocs.hsapiens.dbsnp144.grch37

and update with::

   mamba update bioconductor-snplocs.hsapiens.dbsnp144.grch37

To create a new environment, run:

mamba create --name myenvname bioconductor-snplocs.hsapiens.dbsnp144.grch37

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-snplocs.hsapiens.dbsnp144.grch37:<tag>

(see `bioconductor-snplocs.hsapiens.dbsnp144.grch37/tags`_ for valid values for ``<tag>``)

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