- recipe bioconductor-regutools
regutools: an R package for data extraction from RegulonDB
- Homepage:
https://bioconductor.org/packages/3.16/bioc/html/regutools.html
- License:
Artistic-2.0
- Recipe:
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¶
-
- Versions:
1.10.0-0
,1.6.0-0
,1.4.0-0
,1.2.3-0
,1.2.0-0
,1.0.1-0
- Depends:
bioconductor-annotationdbi
>=1.60.0,<1.61.0
bioconductor-annotationhub
>=3.6.0,<3.7.0
bioconductor-biocfilecache
>=2.6.0,<2.7.0
bioconductor-biostrings
>=2.66.0,<2.67.0
bioconductor-genomicranges
>=1.50.0,<1.51.0
bioconductor-gviz
>=1.42.0,<1.43.0
bioconductor-iranges
>=2.32.0,<2.33.0
bioconductor-rcy3
>=2.18.0,<2.19.0
bioconductor-s4vectors
>=0.36.0,<0.37.0
r-base
>=4.2,<4.3.0a0
- Required By:
Installation
With an activated Bioconda channel (see set-up-channels), install with:
conda install bioconductor-regutools
and update with:
conda update bioconductor-regutools
or use the docker container:
docker pull quay.io/biocontainers/bioconductor-regutools:<tag>
(see bioconductor-regutools/tags for valid values for
<tag>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-regutools/README.html)