Individual skill

spatial-transcriptomics-cell-cell-communication

Spatial cell-cell communication / ligand-receptor (LR) interaction analysis, one skill for every route: LIANA consensus ranking between annotated cell types, CellPhoneDB v5 permutation p-values, DEG method and spatial microenvironments, squidpy neighbourhood enrichment to keep spatially adjacent sender-receiver pairs, LIANA bivariate local LR scores on the tissue (works on Visium spots without labels), pathway-focused candidate evidence tables (immune checkpoints, chemokines, Notch, Wnt, TGF-beta) with contact vs secreted classes and PubMed co-mentions, and multi-sample Tensor-cell2cell and MISTy models. Xenium/MERFISH/CosMx cells, Visium spots, scRNA-seq. Route-specific steps follow the main workflow. Needs cell type labels first (spatial-transcriptomics-cell-type-annotation or a deconvolution skill).

skills/genomics-bioinformatics/spatial-transcriptomics/spatial-transcriptomics-cell-cell-communication/SKILL.md

Source commit 55c1bd3e863d11bf5a853d24bcdda10c88e6eddf

What was checked

Matches the observed repository HEAD

Yes

Scanner rules are current

Yes

Repository scan complete

No

Skill scan complete

No

Observed behavior

Network or broad shell

Last checked

Nov 5, 2026

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