Package Recipe 'mutopia'

recipe mutopia

Topographic modeling of mutational signatures across the cancer genome

Homepage:: https://github.com/sigscape/MuTopia
Documentation:: https://sigscape.github.io/MuTopia/
License:: BSD / BSD-3-Clause
Recipe:: /mutopia/meta.yaml

MuTopia learns topographic models of somatic mutation — it simultaneously decomposes a cancer cohort's mutations into signatures and explains how local genomic context (chromatin state, replication timing, transcription level, DNA sequence composition) shapes each signature's activity across 10 kb windows genome-wide. Provides G-Tensor data structures, SHAP-based feature interpretability, and per-mutation VCF annotation.

package mutopia¶

Versions:

1.0.6-0, 1.0.4-0

Depends:

on bcftools
on bedtools
on click
on colorlog >=6.0.0
on htslib
on luigi >=3.3.0
on matplotlib-base >=3.5,<4
on netcdf4 >=1.7.1.post2,<2
on numba >=0.60.0,<1
on numpy >=1.21
on optuna >=3.4.0,<5
on pandas >=2.1.0
on pydantic >=2.0.0
on pyfaidx
on python >=3.11,<3.12
on pyyaml >=6.0.0
on scikit-learn 1.4.2
on scipy >=1.7,<2
on sparse >=0.15.4
on tabulate
on tqdm
on ucsc-bigwigaverageoverbed
on xarray 2024.9.0

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 mutopia

to add into an existing workspace instead, run:

pixi add mutopia

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 mutopia

Alternatively, to install into a new environment, run:

conda create -n envname mutopia

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/mutopia:<tag>

(see mutopia/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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/mutopia/README.html)