multiomeR 1.2.2

multiomeR 1.2.2 is the release that the multiomeR manuscript cites. It redesigns the manuscript figures, labels the islet cluster and narrows the GWAS panel of the public example mixed_human_31x, and corrects, clarifies and references the methods text of the manual. Only code comments changed in the pipeline code, so the results of your aggregations do not change and nothing in your stores reruns.

What you need to do

1. Update to this release. Releases tag stable, validated commits, so update to the tag rather than pulling main, which can carry development work that is not yet validated. Commit or stash local changes first; resolve any merge conflicts as usual. While no other R process uses the environment, run:

   cd multiomeR  # your clone
   git fetch origin tag v1.2.2
   git merge --ff --no-edit v1.2.2
   pixi install --locked --run-post-link-scripts
   pixi run --use-environment-activation-cache install-r-github-packages

   Nothing else is required: the environment and the parameter schema are unchanged.

2. Coming from 1.1.0? Also follow steps 2 to 6 of the 1.2.0 notes.

What happens to your aggregations

• Existing stores stay current. No pipeline function or target changed, since targets ignores the new code comments, and configuration/ is unchanged.
• In configuration_dev/, mixed_human_31x reruns its WNN cell-type labels and everything downstream of them, and its genetic enrichment module drops 13 studies. The manuscript targets of pipeline_manuscript_figures/targets.R rerun; Figure 1's panel targets are renamed after their new letters.

What changed

Public example

• Islet cells: the WNN labels of mixed_human_31x score an islet endocrine set (INS, SLC30A8, PCSK2, ABCC8, KCNMB2) instead of the beta-cell set, through aggregation_WNN_marker_genes. The islet cluster (371 nuclei, almost all from pancreas) tied beta and acinar cells on ambient INS and stayed unassigned; it is now labelled, and no other cluster changes. The example has 19 cell types.
• GWAS panel: the genetic enrichment module tests 26 instead of 39 studies. Studies with fewer than 20 effective peaks in the aggregation, (Σw)²/Σw² of their variant-weighted peaks, are left out, because their enrichments rest on one or a few loci, as is FastingGlucose_Chen2023, whose samples FastingGlucose_Jee2025 contains. 12 studies are enriched in at least one of 10 cell types.

Manuscript results

• Figure 1 opens with a marker panel (A): for each WNN cell type, the configured marker gene whose expression and promoter accessibility, in cell-type pseudobulks summed over donors, are most specific to it. The other panels move one letter on. Panel D orders its cell types like panel A and its traits by their selected cell type, so the selected pairs form a staircase. Panels E and F show colorectal cancer only, side by side, so the figure fits one page, and F labels only the cell types enriched for it. The panels have tidier labels and ticks, and an empty locus window names the Open Targets locus-to-gene prediction.
• Supplementary Figure S2 shows multiomeR with its Seurat/Signac export against the Seurat/Signac baseline, the measure that matches the baseline's output, in four tagged panels with direct line labels and the fold difference wherever the lines are far enough apart; its units are CPU-hours and GB-hours.
• Supplementary Figure S3 and the Table S3 data follow the 26 studies. S3 keeps only the trait-category and loci tracks, since Table S3 gives each study's method, sample size and ancestry, and fits a portrait page. Supplementary Table S4 counts nuclei.

Documentation

• The workflow overview is redrawn on one grid with lighter styling, heads its primary module like the downstream modules and numbers the module's four parts.
• The methods pages are checked against the code: they state that genetic enrichment uses the 95% credible sets, that differential pseudobulks are not those of the Seurat/Signac export, when the TF-expression comparison is available, which models the paired-cell-type route uses, and how WNN annotation draws its own controls. They give the key defaults of peak–gene filtering, SCAVENGE, doublet removal and clustering, and drop details that the manual gives elsewhere.
• The methods pages also spell out the differential-analysis abbreviations, give each peak–gene support preset its own clause, and cite HNSW, SCTransform v2, SuSiE-inf, PICS, the Open Targets locus-to-gene score and Kenward–Roger inference, with complete author lists and issue numbers.
• The methods pages are easier to read: sentences are short and free of semicolons, everyday words replace jargon, and short reasons accompany choices a reader may question, such as one overdispersion value for all genes, per-group peak calling, the measurement-support filter for peak–gene pairs and joint SuSiE fine-mapping.
• The methods pages cite the published work behind statements that lacked a reference, among them AMULET's threshold, the cell-cycle gene sets, UMAP, the genome blacklist, ArchR's peak rules, depth-normalized peak scores, the edgeR and limma procedures (TMM, voom, duplicateCorrelation, quasi-likelihood F-tests, robust empirical Bayes), MSigDB Hallmark and Reactome, Cicero co-accessibility and the trade-off of batch correction.
• The README shows how to update a clone to a release tag, by merging rather than rebasing, and states the versioning rules. Release notes now live on the GitHub releases page only, which already carried the same notes; NEWS.md is gone from main, and tags up to v1.2.1 keep it.

Development

• Code comments credit the methods that multiomeR adapts, such as AMULET, UCell, Seurat WNN, SCAVENGE, analytic Pearson residuals and ArchR-style consensus peaks, and record the reasons for key design choices. No function changed.
• The release convention moved from dev/RELEASES.md into the README and the release skill, and the documentation rules from AGENTS.md into a documentation skill. CONTRIBUTING.md lists the BPCells convention check among the CI checks.
• The agent skills share one wording with the private repository's, and stale agent guidance and a finished review checklist were removed.