:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'r-loom' .. highlight: bash r-loom ====== .. conda:recipe:: r-loom :replaces_section_title: :noindex: An interface for the single\-cell RNAseq\-oriented loom format. Loom files are an HDF5\-based format for storing and interacting with large single\-cell RNAseq datasets. loomR provides an interface for working with loom files in a loom\-specific way\; we provide routines for validating loom files\, iterating with chunks through data within the loom file\, and provide a platform for other packages to build support for loom files. :homepage: https://github.com/mojaveazure/loomR :license: GPL3 / GPL-3 :recipe: /`r-loom `_/`meta.yaml `_ .. conda:package:: r-loom |downloads_r-loom| |docker_r-loom| :versions: ``0.2.0.2-6``,  ``0.2.0.2-5``,  ``0.2.0.2-4``,  ``0.2.0.2-3``,  ``0.2.0.2-2``,  ``0.2.0.2-1``,  ``0.2.0.2-0``,  ``0.2.0.1-0`` :depends icu: ``>=64`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-hdf5r: :depends r-iterators: :depends r-itertools: :depends r-matrix: :depends r-pbapply: :depends r-stringr: :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 r-loom and update with:: mamba update r-loom To create a new environment, run:: mamba create --name myenvname r-loom 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/r-loom: (see `r-loom/tags`_ for valid values for ````) .. |downloads_r-loom| image:: https://img.shields.io/conda/dn/bioconda/r-loom.svg?style=flat :target: https://anaconda.org/bioconda/r-loom :alt: (downloads) .. |docker_r-loom| image:: https://quay.io/repository/biocontainers/r-loom/status :target: https://quay.io/repository/biocontainers/r-loom .. _`r-loom/tags`: https://quay.io/repository/biocontainers/r-loom?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/r-loom/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/r-loom/README.html