- recipe bioconductor-vcfarray
Representing on-disk / remote VCF files as array-like objects
VCFArray extends the DelayedArray to represent VCF data entries as array-like objects with on-disk / remote VCF file as backend. Data entries from VCF files, including info fields, FORMAT fields, and the fixed columns (REF, ALT, QUAL, FILTER) could be converted into VCFArray instances with different dimensions.
- package bioconductor-vcfarray¶
- depends bioconductor-biocgenerics:
- depends bioconductor-delayedarray:
- depends bioconductor-genomicfiles:
- depends bioconductor-genomicranges:
- depends bioconductor-rsamtools:
- depends bioconductor-s4vectors:
- depends bioconductor-variantannotation:
- 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-vcfarray and update with:: mamba update bioconductor-vcfarray
To create a new environment, run:
mamba create --name myenvname bioconductor-vcfarray
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-vcfarray:<tag> (see `bioconductor-vcfarray/tags`_ for valid values for ``<tag>``)