nanomix 0.2.0-foss-2023a

Nanomix: Methylation Deconvolution of Nanopore Sequencing Data. Methylation deconvolution is the process of determining the proportion of distinct cell types in a complex (hetergeneic) mixture of cell or cell free DNA. This tool provides suitable models for performing deconvolution on Nanopore sequencing data. In particular our new models account for the non-uniform coverage distribution and high error rate in modified base calling. We also include more typical deconvolution models for deconvolution of bisulfite sequencing data or bead chip arrays.

Accessing nanomix 0.2.0-foss-2023a

To load the module for nanomix 0.2.0-foss-2023a please use this command on the BEAR systems (BlueBEAR and BEAR Cloud VMs):

📋 module load bear-apps/2023a
module load nanomix/0.2.0-foss-2023a

BEAR Apps Version

2023a

Architectures

EL8-emeraldrapids — EL8-icelake — EL8-sapphirerapids

The listed architectures consist of two parts: OS-CPU. The OS used is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.

Extensions

• nanomix 0.2.0
• natsort 8.4.0
• ncls 0.0.68
• pyranges 0.0.120
• pyrle 0.0.42
• ray 2.46.0
• sorted_nearest 0.0.39

More Information

For more information visit the nanomix website.

Dependencies

This version of nanomix has a direct dependency on: foss/2023a matplotlib/3.7.2-gfbf-2023a maturin/1.4.0-GCCcore-12.3.0-Rust-1.75.0 protobuf-python/4.24.0-GCCcore-12.3.0 Python/3.11.3-GCCcore-12.3.0 Python-bundle-PyPI/2023.06-GCCcore-12.3.0 PyYAML/6.0-GCCcore-12.3.0 SciPy-bundle/2023.07-gfbf-2023a

Last modified on 10th June 2025