recipe bioconductor-variantexperiment

A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/VariantExperiment.html

License:

GPL-3

Recipe:

/bioconductor-variantexperiment/meta.yaml

VariantExperiment is a Bioconductor package for saving data in VCF/GDS format into RangedSummarizedExperiment object. The high-throughput genetic/genomic data are saved in GDSArray objects. The annotation data for features/samples are saved in DelayedDataFrame format with mono-dimensional GDSArray in each column. The on-disk representation of both assay data and annotation data achieves on-disk reading and processing and saves memory space significantly. The interface of RangedSummarizedExperiment data format enables easy and common manipulations for high-throughput genetic/genomic data with common SummarizedExperiment metaphor in R and Bioconductor.

package bioconductor-variantexperiment

versions:

1.16.0-0,  1.14.0-0,  1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0

depends bioconductor-delayeddataframe:

>=1.18.0,<1.19.0

depends bioconductor-gdsarray:

>=1.22.0,<1.23.0

depends bioconductor-gdsfmt:

>=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 bioconductor-seqarray:

>=1.42.0,<1.43.0

depends bioconductor-snprelate:

>=1.36.0,<1.37.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

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-variantexperiment

and update with::

   mamba update bioconductor-variantexperiment

To create a new environment, run:

mamba create --name myenvname bioconductor-variantexperiment

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-variantexperiment:<tag>

(see `bioconductor-variantexperiment/tags`_ for valid values for ``<tag>``)

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