- recipe bioconductor-regutools
regutools: an R package for data extraction from RegulonDB
RegulonDB has collected, harmonized and centralized data from hundreds of experiments for nearly two decades and is considered a point of reference for transcriptional regulation in Escherichia coli K12. Here, we present the regutools R package to facilitate programmatic access to RegulonDB data in computational biology. regutools provides researchers with the possibility of writing reproducible workflows with automated queries to RegulonDB. The regutools package serves as a bridge between RegulonDB data and the Bioconductor ecosystem by reusing the data structures and statistical methods powered by other Bioconductor packages. We demonstrate the integration of regutools with Bioconductor by analyzing transcription factor DNA binding sites and transcriptional regulatory networks from RegulonDB. We anticipate that regutools will serve as a useful building block in our progress to further our understanding of gene regulatory networks.
- package bioconductor-regutools¶
- depends bioconductor-annotationdbi:
- depends bioconductor-annotationhub:
- depends bioconductor-biocfilecache:
- depends bioconductor-biostrings:
- depends bioconductor-genomicranges:
- depends bioconductor-gviz:
- depends bioconductor-iranges:
- depends bioconductor-rcy3:
- depends bioconductor-s4vectors:
- depends r-base:
- depends r-dbi:
- depends r-rsqlite:
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-regutools and update with:: mamba update bioconductor-regutools
To create a new environment, run:
mamba create --name myenvname bioconductor-regutools
myenvnamebeing 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-regutools:<tag> (see `bioconductor-regutools/tags`_ for valid values for ``<tag>``)