multiomeR 0.5.0

multiomeR 0.5.0 (2026-09-11)

Released through PR #5.

This release changes cluster annotations, cluster IDs, peak–gene inference and
several target/output names. Review the migration notes before rerunning an
existing analysis.

QC and interpretation

• Organize review outputs into eight numbered QC checkpoints, separating GEX
  PCA and ATAC LSI review from clustering. Add cumulative, per-action nuclei
  retention flows and validate matching gene definitions before aggregation.
• Select QC violin metrics from the shared manifest. Correct UpSet percentages,
  align RNA/ATAC/WNN confusion matrices, improve marker-set dot plots, and show
  all computed PCA/LSI dimensions in review plots.
• Add within-cell-type cluster-marker comparisons and volcano plots. Number
  GEX, ATAC and WNN Leiden clusters by decreasing size without changing their
  membership; break size ties by the original cluster ID.
• Add readable motif-family labels, palettes that accommodate many cell groups,
  and aligned genetic-enrichment panels and shared legends.

Cluster annotation

• Replace the former standardized module-score labeller with matched-control
  UCell evidence across GEX, ATAC and WNN. All three use a shared GEX control
  reference. There is one annotation method, with no legacy selector.
• Assign the leading label only when its adjusted score exceeds both matched
  background and competing labels by aggregation_cluster_annotation_min_advantage
  (default 0.05). Otherwise retain Unassigned, the candidate and a reason.
  Stability and GEM-well agreement are diagnostics, not assignment gates.
• Preserve positive and negative UCell marker signatures. Signed scores are
  clipped per cell before averaging for observed and control signatures,
  including marker-deletion diagnostics. Positive-only panels retain the
  faster exact rank-summary calculation.
• Export cluster evidence, marker-set support and competition, and clearer
  pre-doublet-filtering review plots. Unassigned clusters remain separate for
  doublet detection. Adjusted scores are not identity probabilities or validated
  biological error rates.

Peak–gene analysis

• Allow exploratory discovery with few donors, including one donor, when
  aggregate counts and residual variation permit estimation. Adjust for donor
  and library depth; report conditional HC3 association statistics and separate
  donor-support diagnostics. State is no longer a nuisance-design term.
• Retain nonpromoter gene-body candidates and plot the donor/depth residuals
  used in scoring. These associations do not establish population-level
  replication or causal enhancer–gene relationships.
• Add SuSiE conditional peak prioritization and compact global-FDR reconstruction
  from chromosome branch inputs. Handle empty candidate sets with explicit
  plot outputs. SuSiE PIPs remain exploratory conditional prioritization.

Migration

• Remove aggregation_cluster_annotation_method and
  aggregation_allow_multiple_cell_types from configuration. Signed marker
  panels remain supported; check the new evidence before interpreting labels.
• Recheck external references to numeric cluster IDs. Annotation changes can
  propagate through doublet grouping, retained cells and downstream analyses.
• Find plots and compatibility exports in numbered checkpoint folders, including
  GEX_Seurat_object.3_GEX_QC and multimodal_Seurat_object.8_multimodal_QC.
  Update scripts selecting the former target names. Old output files are not
  automatically deleted; consult current target metadata when reviewing results.
• Subgroup reprocessing is removed from the public workflow. Remove its six
  aggregation_subgroups_*/contamination-filter settings from public configs.
• Peak–gene results replace cluster_robust_SE with association_SE and add
  donor-support and inference-status fields. Recompute affected targets before
  comparing results; this is a method change, not just a speed improvement.

Principal recomputation boundaries (destination manifests provide full names):

cascading_target_breaking: cell_retention_tibble.GEX_input
cascading_target_breaking: QC_metric_manifest_tsv
cascading_target_breaking: PCA_clusters.GEX
cascading_target_breaking: LSI_clusters.ATAC
cascading_target_breaking: clusters_tibble_raw.WNN
cascading_target_breaking: metadata_w_cell_types_unfiltered_tibble.GEX
cascading_target_breaking: metadata_w_cell_types_unfiltered_tibble.ATAC
cascading_target_breaking: metadata_w_cell_types_tibble.WNN
cascading_target_breaking: peak_gene_correlation_donor_state_records.peak_gene_correlation.WNN
contained_target_breaking: GEX_Seurat_object.3_GEX_QC
contained_target_breaking: multimodal_Seurat_object.8_multimodal_QC

Validation

Public algorithm CI and documentation builds passed on the release implementation
at 43dac20; the final preparation commit changes only the release date and PR
link. Focused numerical validation includes 91 passing scoring/peak-gene
assertions, signed UCell parity and a nonempty SuSiE smoke fit. Default and
peak-gene opt-in manifests and both documentation books were validated.
See the validation record
for evidence and limits. No full demo/cohort pipeline replay was performed.