Release multiomeR 1.1.0 · koefoeden/multiomeR

A documentation and demo release. The public demo aggregation is rebuilt with new data and markers; other aggregations need no recomputation.

Demo

Combine two healthy PBMC GEM wells from the same 10x Genomics series in the demo: the granulocyte-sorted well as before and the unsorted 3k well, now unsorted_PBMC_human, which replaces the lymphoma lymph node. The download shrinks from about 4.1 to 1.3 GB and the stored results from about 6.4 to 3.3 GB.
Annotate the demo with marker sets whose genes single nuclei capture: B, Mono, NK, DC and T. The previous two-gene markers left most demo nuclei Unassigned; every GEX, ATAC and WNN cluster is now labeled.
Plot only the sorting annotation in the demo's categorical UMAPs, because its other GEM-well annotations are now constant.

Merge the implementation book into the manual. Its method descriptions form an In depth part with one primary-module page organized by checkpoint stage, one page per optional module and the algorithm-validation page; the implementation conventions become one Change the pipeline page. Each checkpoint of the running guide and each module page links to its methods.
Mark the reading layers in the sidebar: the guides, a Reference part that now includes the parameter browser, and the In depth part with an advanced badge.
Show the printed results of every command on the demo-results page, refreshed from the built demo with pixi run refresh-demo-outputs.
Give the GEM well, donor and aggregation reference pages one layout, and document pooled GEM wells, the rules checked and when, and aggregation inheritance.
Use US spelling throughout the manual.
Deploy the documentation only from main.

Retry each live preflight check of validate-local up to four times, also after refused connections, so an intermittent outage of a remote source no longer fails the whole validation.

Run pixi run --use-environment-activation-cache setup-demo again to download the new demo well; example_data/lymphoma_lymph_human is no longer used and can be deleted.
Target invalidation: every immune_human_2x target and the per-GEM-well targets of unsorted_PBMC_human build anew. Changed target descriptions invalidate nothing, so other aggregations stay current.