Wrap Liana toolkit for Single-cell and Spatial Transcriptomics

tools/liana/.shed.yml

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+name: liana
+owner: iuc
+description: "LIANA+ - Ligand-receptor analysis framework"
+homepage_url: https://liana-py.readthedocs.io
+long_description: |
+    LIANA+ is a scalable framework for cell-cell communication analysis. It includes ligand-receptor inference methods, spatial analysis with bivariate metrics, and multi-view spatial modelling with MISTy.
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/liana
+type: unrestricted
+categories:
+  - Single Cell
+  - Spatial Omics
+  - Transcriptomics
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper for the LIANA+ tool suite: {{ tool_name }}"
+suite:
+  name: "suite_liana"
+  description: "LIANA+ - Ligand-receptor analysis framework"
+  long_description: |
+    LIANA+ is a scalable framework for cell-cell communication analysis. It includes ligand-receptor inference methods, spatial analysis with bivariate metrics, and multi-view spatial modelling with MISTy.

tools/liana/README.md

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+LIANA+
+======
+
+Galaxy tools for [LIANA+](https://liana-py.readthedocs.io/), a framework for cell-cell communication analysis.
+
+## Tools
+
+### 1. Single Cell Methods (`single_cell.xml`)
+
+Ligand-receptor inference methods for single-cell data.
+
+Method | Description
+--- | ---
+`cellchat` | CellChat ligand-receptor method
+`cellphonedb` | CellPhoneDB ligand-receptor method
+`connectome` | Connectome ligand-receptor method
+`logfc` | Log fold change ligand-receptor method
+`natmi` | NATMI ligand-receptor method
+`singlecellsignalr` | SingleCellSignalR ligand-receptor method
+`geometric_mean` | Geometric mean ligand-receptor method
+`rank_aggregate` | Aggregate rankings from multiple methods
+
+### 2. Spatial Methods (`spatial.xml`)
+
+Spatial ligand-receptor analysis using bivariate metrics.
+
+Method | Description
+--- | ---
+`bivariate` | Bivariate local spatial metrics for ligand-receptor analysis
+
+#### Bivariate Metrics
+
+**Local metrics:**
+
+Metric | Description
+--- | ---
+`cosine` | Weighted cosine similarity
+`jaccard` | Weighted Jaccard similarity
+`pearson` | Weighted Pearson correlation
+`spearman` | Weighted Spearman correlation
+`masked_spearman` | Masked and weighted Spearman correlation
+`product` | Simple weighted product
+`norm_product` | Normalized weighted product
+`morans` | Moran's R
+
+**Global metrics:**
+
+Metric | Description
+--- | ---
+`morans` | Moran's I (global spatial autocorrelation)
+`lee` | Lee's L (bivariate spatial association)
+
+### 3. Spatial Relationships (`spatial_relationships.xml`)
+
+Multi-view spatial modelling with MISTy.
+
+Method | Description
+--- | ---
+`genericMistyData` | Generic MISTy multi-view modelling
+`lrMistyData` | Ligand-receptor MISTy modelling
+
+#### MISTy Models
+
+Model | Description
+--- | ---
+`RandomForestModel` | Random Forest (uses out-of-bag predictions)
+`LinearModel` | Linear regression (uses cross-validation)
+`RobustLinearModel` | Robust linear regression
+
+#### Kernel Functions
+
+Kernel | Description
+--- | ---
+`misty_rbf` | MISTy RBF kernel (Gaussian derivative)
+`gaussian` | Gaussian kernel
+`exponential` | Exponential kernel
+`linear` | Linear kernel
+
+### 4. Plotting (`plot.xml`)
+
+Visualization tools for LIANA results.
+
+Method | Description
+--- | ---
+`dotplot` | Dot plot of ligand-receptor interactions
+`tileplot` | Tile plot of interactions
+`connectivity` | Spatial connectivity visualization
+
+### 5. Available Resources
+
+Built-in ligand-receptor resources from `li.resource.show_resources()`:
+
+- `consensus` (default)
+- `baccin2019`
+- `cellcall`
+- `cellchatdb`
+- `cellinker`
+- `cellphonedb`
+- `celltalkdb`
+- `connectomedb2020`
+- `embrace`
+- `guide2pharma`
+- `hpmr`
+- `icellnet`
+- `italk`
+- `kirouac2010`
+- `lrdb`
+- `mouseconsensus`
+- `ramilowski2015`
+
+## References
+
+- Dimitrov, D., Türei, D., Garrido-Rodriguez, M. et al. Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. Nat Commun 13, 3224 (2022). https://doi.org/10.1038/s41467-022-30755-0
+- Tanevski, J., Flores, R.O.R., Gabor, A. et al. Explainable multiview framework for dissecting spatial relationships from highly multiplexed data. Genome Biol 23, 97 (2022).
+- [LIANA+ Documentation](https://liana-py.readthedocs.io/)
+- [LIANA+ GitHub](https://github.com/saezlab/liana-py)