recipe pylocuszoom

Publication-ready GWAS visualization library with regional association plots, gene tracks, eQTL, PheWAS, fine-mapping, and forest plots

Homepage:

https://github.com/michael-denyer/pylocuszoom

License:

GPL3 / GPL-3.0-or-later

Recipe:

/pylocuszoom/meta.yaml

pyLocusZoom creates publication-quality genetic association visualizations: regional association plots with LD coloring and recombination overlays, stacked multi-GWAS comparisons, eQTL overlays, fine-mapping/SuSiE credible sets, PheWAS (phenome-wide association) plots, and forest plots for meta-analysis. Includes gene track visualization, file loaders for common formats (REGENIE, BOLT-LMM, SAIGE, GEMMA, GTEx, SuSiE, FINEMAP), and three backends: matplotlib (static/publication), plotly (interactive), and bokeh (dashboards).

package pylocuszoom

versions:

1.3.2-0,  1.3.1-0,  1.2.0-0,  1.1.2-0,  1.0.0-0

depends adjusttext:

>=0.8

depends bokeh:

>=3.8.2

depends colorcet:

>=3.0.0

depends loguru:

>=0.7.0

depends matplotlib-base:

>=3.5.0

depends numpy:

>=1.21.0

depends pandas:

>=1.4.0

depends plotly:

>=5.15.0

depends pydantic:

>=2.0.0

depends pyliftover:

>=0.4

depends python:

>=3.10

depends python-kaleido:

>=0.2.0

depends requests:

>=2.25.0

depends tqdm:

>=4.60.0

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

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 pylocuszoom

and update with::

   mamba update pylocuszoom

To create a new environment, run:

mamba create --name myenvname pylocuszoom

with myenvname being 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/pylocuszoom:<tag>

(see `pylocuszoom/tags`_ for valid values for ``<tag>``)

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