recipe bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor

Full genome sequences for Homo sapiens (UCSC version hg38, based on GRCh38.p12) with injected minor alleles (dbSNP151)

Homepage:

https://bioconductor.org/packages/3.18/data/annotation/html/BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor.html

License:

CC BY-NC-ND 4.0

Recipe:

/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor/meta.yaml

Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with minor alleles injected from dbSNP151, and stored in Biostrings objects. Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with minor alleles injected from dbSNP151, and stored in Biostrings objects. Only common single nucleotide variants (SNVs) with at least one alternate allele with frequency greater than 0.01 were considered. For SNVs with more than 1 alternate allele, the most frequent allele was chosen as the minor allele to be injected into the reference genome.

package bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor

(downloads) docker_bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor

versions:

0.0.9999-4,  0.0.9999-3,  0.0.9999-2,  0.0.9999-1,  0.0.9999-0

depends bioconductor-bsgenome:

>=1.70.0,<1.71.0

depends bioconductor-data-packages:

>=20231203

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-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor

and update with::

   mamba update bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor

To create a new environment, run:

mamba create --name myenvname bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor

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-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor:<tag>

(see `bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor/tags`_ for valid values for ``<tag>``)

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