Package Recipe 'bioconductor-compounddb'

recipe bioconductor-compounddb

Creating and Using (Chemical) Compound Annotation Databases

Homepage:: https://bioconductor.org/packages/3.20/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.

package bioconductor-compounddb¶

Versions:

1.14.2-0, 1.10.0-0, 1.6.0-0, 1.4.0-0, 1.2.0-0

Depends:

on bioconductor-annotationfilter >=1.34.0,<1.35.0
on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-chemminer >=3.62.0,<3.63.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-metabocoreutils >=1.18.0,<1.19.0
on bioconductor-mscoreutils >=1.22.0,<1.23.0
on bioconductor-protgenerics >=1.42.0,<1.43.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-spectra >=1.20.0,<1.21.0
on r-base >=4.5,<4.6.0a0
on r-dbi
on r-dbplyr
on r-dplyr
on r-jsonlite
on r-rsqlite
on r-stringi
on r-tibble
on r-xml2

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-compounddb

to add into an existing workspace instead, run:

pixi add bioconductor-compounddb

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-compounddb

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-compounddb

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-compounddb:<tag>

(see bioconductor-compounddb/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an 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)