- recipe bioconductor-rsemmed
An interface to the Semantic MEDLINE database
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/rsemmed.html
- License:
Artistic-2.0
- Recipe:
A programmatic interface to the Semantic MEDLINE database. It provides functions for searching the database for concepts and finding paths between concepts. Path searching can also be tailored to user specifications, such as placing restrictions on concept types and the type of link between concepts. It also provides functions for summarizing and visualizing those paths.
- package bioconductor-rsemmed¶
- Versions:
1.20.0-0,1.16.0-0,1.12.0-0,1.10.0-0,1.8.0-0,1.4.0-0,1.2.0-0,1.0.0-1,1.0.0-0- Depends:
on r-base
>=4.5,<4.6.0a0on r-dplyr
on r-igraph
on r-magrittr
on r-stringr
- 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-rsemmed
to add into an existing workspace instead, run:
pixi add bioconductor-rsemmed
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-rsemmed
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-rsemmed
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-rsemmed:<tag>
(see bioconductor-rsemmed/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:
[](http://bioconda.github.io/recipes/bioconductor-rsemmed/README.html)
