1. Load the prepared SpatialGraph | 2. Tissue layout | 3. Find size-2 and size-3 motifs | 4. Where does a motif live in space? | 5. Enrichment under a global label-permutation null | 6. Region-stratified vs unstratified | 7. Top-enriched motif → associated genes | 8. Per-sample meta-analysis | 9. Per-niche motif distributions | 10. Niche-defining motifs in physical space | 11. Cross-niche bridging motifs | 12. Bar chart of the most common size-3 motifs | What's next
Package: smotif 0.2.0
Ruben Dries
smotif: Spatial Multi-Cellular Motifs
Discovery and statistical evaluation of recurrent multi-cellular motifs (size 2, 3, and 4) in spatial omics data. Provides a lightweight 'SpatialGraph' representation backed by parquet, enumeration over igraph, spatially-aware null models, motif-to-gene association, and cross-region or cross-sample comparison. Designed to be framework-agnostic so that the core can be folded into Giotto Suite later.
Authors:
smotif_0.2.0.tar.gz
smotif_0.2.0.zip(r-4.7-any)smotif_0.2.0.zip(r-4.6-any)smotif_0.2.0.zip(r-4.5-any)
smotif_0.2.0.tgz(r-4.6-any)smotif_0.2.0.tgz(r-4.5-any)
smotif_0.2.0.tar.gz(r-4.7-any)smotif_0.2.0.tar.gz(r-4.6-any)
smotif_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
smotif/json (API)
| # Install 'smotif' in R: |
| install.packages('smotif', repos = c('https://drieslab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/drieslab/smotif/issues
Last updated from:4869780ba7. Checks:7 ERROR, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | ERROR | 156 | ||
| source / vignettes | OK | 283 | ||
| linux-release | ERROR | 166 | ||
| macos-release | ERROR | 167 | ||
| macos-oldrel | ERROR | 189 | ||
| windows-devel | ERROR | 133 | ||
| windows-release | ERROR | 185 | ||
| windows-oldrel | ERROR | 125 | ||
| wasm-release | OK | 152 |
Exports:as_igraphassociate_genesbuild_spatial_graphcompare_motifsfind_motifsmotif_enrichmentmotif_enrichment_storemotif_enrichment_streammotif_instancesMotifsread_spatial_graphSpatialGraphstore_node_ordersubset_regionsubset_sampletest_motif_enrichmentwrite_spatial_graph
Dependencies:arrowassertthatbitbit64clicpp11data.tableglueigraphlatticelifecyclemagrittrMatrixpkgconfigpurrrR6rlangtidyselectvctrswithr
