- recipe regain-cli
Bayesian-network pipeline for ARG/virulence co-occurrence analysis.
- Homepage:
- License:
MIT
- Recipe:
ReGAIN is a reproducible CLI for quantifying co-occurrence among bacterial antibiotic/heavy metal resistance and virulence genes using Bayesian network structure learning (bnlearn/gRain) and post-hoc metrics. It includes dataset curation, visualization, and multivariate analysis.
- package regain-cli¶
- Versions:
1.7.1-0,1.6.3-0,1.6.2-0- Depends:
on bioconductor-graph
on biopython
>=1.83on blast
on ncbi-amrfinderplus
on pandas
on python
>=3.10on r-ape
on r-base
>=4.4on r-bnlearn
on r-cluster
on r-compositions
on r-doparallel
on r-dplyr
on r-ellipse
on r-foreach
on r-ggplot2
on r-ggraph
on r-ggrepel
on r-grain
on r-igraph
on r-optparse
on r-pbapply
on r-progressr
on r-rcolorbrewer
on r-reshape2
on r-scales
on r-tibble
on r-tidygraph
on r-tidyr
on r-vegan
on r-visnetwork
on tqdm
>=4.67
- 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 regain-cli
to add into an existing workspace instead, run:
pixi add regain-cli
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 regain-cli
Alternatively, to install into a new environment, run:
conda create -n envname regain-cli
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/regain-cli:<tag>
(see regain-cli/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/regain-cli/README.html)
