multiomeR is a targets-based workflow for processing and analyzing single-nucleus 10x Genomics Multiome data. It is designed as a lean, readable framework that users can adapt to their own studies rather than as a black-box command-line pipeline.
The active workflow is a single root targets project driven by _targets.R, cfg_GEM_wells.tsv, and cfg_aggregations.yaml.
multiomeR is in beta. The workflow is actively changing, and public interfaces may still change.
The user manual is built from the Quarto book in website/. It includes a quickstart guide, an output gallery and full implementation details: https://koefoeden.github.io/multiomeR/
- Linux system with at least 60 GB of RAM, preferably equipped with a job-scheduler supported by the crew.cluster package: SLURM, PBS, SGE or LSf.
Bug reports and broadly useful feature requests are welcome, especially when they affect users analyzing 10x Multiome data. The project prioritizes lean, inspectable workflow changes over broad abstractions or site-specific convenience layers. See .github/CONTRIBUTING.md.