- recipe bioconductor-bsgenome.hsapiens.ucsc.hg38.masked
Full masked genomic sequences for Homo sapiens (UCSC version hg38)
Full genomic sequences for Homo sapiens as provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31). The sequences are the same as in BSgenome.Hsapiens.UCSC.hg38, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default. The sequences are stored in MaskedDNAString objects.
- package bioconductor-bsgenome.hsapiens.ucsc.hg38.masked¶
- depends bioconductor-bsgenome:
- depends bioconductor-bsgenome.hsapiens.ucsc.hg38:
- depends bioconductor-data-packages:
- depends bioconductor-genomeinfodb:
- depends curl:
- depends r-base:
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.masked and update with:: mamba update bioconductor-bsgenome.hsapiens.ucsc.hg38.masked
To create a new environment, run:
mamba create --name myenvname bioconductor-bsgenome.hsapiens.ucsc.hg38.masked
myenvnamebeing 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.masked:<tag> (see `bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/tags`_ for valid values for ``<tag>``)