:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-compounddb' .. highlight: bash bioconductor-compounddb ======================= .. conda:recipe:: bioconductor-compounddb :replaces_section_title: :noindex: Creating and Using \(Chemical\) Compound Annotation Databases :homepage: https://bioconductor.org/packages/3.18/bioc/html/CompoundDb.html :license: Artistic-2.0 :recipe: /`bioconductor-compounddb `_/`meta.yaml `_ CompoundDb provides functionality to create and use \(chemical\) compound annotation databases from a variety of different sources such as LipidMaps\, HMDB\, ChEBI or MassBank. The database format allows to store in addition MS\/MS spectra along with compound information. The package provides also a backend for Bioconductor\'s Spectra package and allows thus to match experimetal MS\/MS spectra against MS\/MS spectra in the database. Databases can be stored in SQLite format and are thus portable. .. conda:package:: bioconductor-compounddb |downloads_bioconductor-compounddb| |docker_bioconductor-compounddb| :versions: ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.0-0`` :depends bioconductor-annotationfilter: ``>=1.26.0,<1.27.0`` :depends bioconductor-biobase: ``>=2.62.0,<2.63.0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-chemminer: ``>=3.54.0,<3.55.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-metabocoreutils: ``>=1.10.0,<1.11.0`` :depends bioconductor-mscoreutils: ``>=1.14.0,<1.15.0`` :depends bioconductor-protgenerics: ``>=1.34.0,<1.35.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-spectra: ``>=1.12.0,<1.13.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-dbi: :depends r-dbplyr: :depends r-dplyr: :depends r-jsonlite: :depends r-rsqlite: :depends r-tibble: :depends r-xml2: :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-compounddb and update with:: mamba update bioconductor-compounddb To create a new environment, run:: mamba create --name myenvname bioconductor-compounddb 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-compounddb: (see `bioconductor-compounddb/tags`_ for valid values for ````) .. |downloads_bioconductor-compounddb| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-compounddb.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-compounddb :alt: (downloads) .. |docker_bioconductor-compounddb| image:: https://quay.io/repository/biocontainers/bioconductor-compounddb/status :target: https://quay.io/repository/biocontainers/bioconductor-compounddb .. _`bioconductor-compounddb/tags`: https://quay.io/repository/biocontainers/bioconductor-compounddb?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-compounddb/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-compounddb/README.html