- recipe strmie-hd
Automated Huntington Disease polyQ pattern scanner.
- Homepage:
- Documentation:
- License:
MIT / MIT
- Recipe:
STRmie-HD (Short Tandem Repeat Mapping and Identification Engine - Huntington's Disease) is an interactive, Python-based tool designed to support the curation, visualization, and interpretation of short tandem repeat (STR) genotyping data obtained from Huntington's Disease (HD) patients. It enables the prediction, refinement and validation of CAG/CCG repeat expansion results in the context of HD, by highlighting cases of allelic instability or potential misclassification.
- package strmie-hd¶
- Versions:
1.0.0-0- Depends:
on biopython
on colorama
on h5py
on jinja2
on joblib
on matplotlib-base
on numpy
on openpyxl
on pandas
on pytest
on python
>=3.8on regex
on scikit-learn
on scipy
on seaborn
on xlrd
- 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 strmie-hd
to add into an existing workspace instead, run:
pixi add strmie-hd
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 strmie-hd
Alternatively, to install into a new environment, run:
conda create -n envname strmie-hd
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/strmie-hd:<tag>
(see strmie-hd/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/strmie-hd/README.html)
