:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-variantexperiment' .. highlight: bash bioconductor-variantexperiment ============================== .. conda:recipe:: bioconductor-variantexperiment :replaces_section_title: :noindex: 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. .. conda:package:: bioconductor-variantexperiment |downloads_bioconductor-variantexperiment| |docker_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: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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: (see `bioconductor-variantexperiment/tags`_ for valid values for ````) .. |downloads_bioconductor-variantexperiment| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-variantexperiment.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-variantexperiment :alt: (downloads) .. |docker_bioconductor-variantexperiment| image:: https://quay.io/repository/biocontainers/bioconductor-variantexperiment/status :target: https://quay.io/repository/biocontainers/bioconductor-variantexperiment .. _`bioconductor-variantexperiment/tags`: https://quay.io/repository/biocontainers/bioconductor-variantexperiment?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-variantexperiment/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-variantexperiment/README.html