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, the settings in configuration/. To select a separate settings directory for your project, use the ignored root configuration.local file.
multiomeR 1.0 is the first stable release. The manuscript describing it is under peer review (link to come).
See release notes and migration steps and the release convention.
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.