recipe bioconductor-compounddb

Creating and Using (Chemical) Compound Annotation Databases

Homepage:

https://bioconductor.org/packages/3.16/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:

1.2.0-0

Depends:

• bioconductor-annotationfilter >=1.22.0,<1.23.0

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-chemminer >=3.50.0,<3.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-metabocoreutils >=1.6.0,<1.7.0

• bioconductor-mscoreutils >=1.10.0,<1.11.0

• bioconductor-protgenerics >=1.30.0,<1.31.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-spectra >=1.8.0,<1.9.0

• r-base >=4.2,<4.3.0a0

• r-dbi

• r-dbplyr

• r-dplyr

• r-jsonlite

• r-rsqlite

• r-tibble

• r-xml2

Required By:

• bioconductor-metaboannotation

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-compounddb

and update with:

conda update bioconductor-compounddb

or use the docker container:

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

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

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