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date Tue, 10 Mar 2026 13:41:01 +0000
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1 LIANA+
2 ======
3
4 Galaxy tools for [LIANA+](https://liana-py.readthedocs.io/), a framework for cell-cell communication analysis.
5
6 ## Tools
7
8 ### 1. Single Cell Methods (`single_cell.xml`)
9
10 Ligand-receptor inference methods for single-cell data.
11
12 Method | Description
13 --- | ---
14 `cellchat` | CellChat ligand-receptor method
15 `cellphonedb` | CellPhoneDB ligand-receptor method
16 `connectome` | Connectome ligand-receptor method
17 `logfc` | Log fold change ligand-receptor method
18 `natmi` | NATMI ligand-receptor method
19 `singlecellsignalr` | SingleCellSignalR ligand-receptor method
20 `geometric_mean` | Geometric mean ligand-receptor method
21 `rank_aggregate` | Aggregate rankings from multiple methods
22
23 ### 2. Spatial Methods (`spatial.xml`)
24
25 Spatial ligand-receptor analysis using bivariate metrics.
26
27 Method | Description
28 --- | ---
29 `bivariate` | Bivariate local spatial metrics for ligand-receptor analysis
30
31 #### Bivariate Metrics
32
33 **Local metrics:**
34
35 Metric | Description
36 --- | ---
37 `cosine` | Weighted cosine similarity
38 `jaccard` | Weighted Jaccard similarity
39 `pearson` | Weighted Pearson correlation
40 `spearman` | Weighted Spearman correlation
41 `masked_spearman` | Masked and weighted Spearman correlation
42 `product` | Simple weighted product
43 `norm_product` | Normalized weighted product
44 `morans` | Moran's R
45
46 **Global metrics:**
47
48 Metric | Description
49 --- | ---
50 `morans` | Moran's I (global spatial autocorrelation)
51 `lee` | Lee's L (bivariate spatial association)
52
53 ### 3. Spatial Relationships (`spatial_relationships.xml`)
54
55 Multi-view spatial modelling with MISTy.
56
57 Method | Description
58 --- | ---
59 `genericMistyData` | Generic MISTy multi-view modelling
60 `lrMistyData` | Ligand-receptor MISTy modelling
61
62 #### MISTy Models
63
64 Model | Description
65 --- | ---
66 `RandomForestModel` | Random Forest (uses out-of-bag predictions)
67 `LinearModel` | Linear regression (uses cross-validation)
68 `RobustLinearModel` | Robust linear regression
69
70 #### Kernel Functions
71
72 Kernel | Description
73 --- | ---
74 `misty_rbf` | MISTy RBF kernel (Gaussian derivative)
75 `gaussian` | Gaussian kernel
76 `exponential` | Exponential kernel
77 `linear` | Linear kernel
78
79 ### 4. Plotting (`plot.xml`)
80
81 Visualization tools for LIANA results.
82
83 Method | Description
84 --- | ---
85 `dotplot` | Dot plot of ligand-receptor interactions
86 `tileplot` | Tile plot of interactions
87 `connectivity` | Spatial connectivity visualization
88
89 ### 5. Available Resources
90
91 Built-in ligand-receptor resources from `li.resource.show_resources()`:
92
93 - `consensus` (default)
94 - `baccin2019`
95 - `cellcall`
96 - `cellchatdb`
97 - `cellinker`
98 - `cellphonedb`
99 - `celltalkdb`
100 - `connectomedb2020`
101 - `embrace`
102 - `guide2pharma`
103 - `hpmr`
104 - `icellnet`
105 - `italk`
106 - `kirouac2010`
107 - `lrdb`
108 - `mouseconsensus`
109 - `ramilowski2015`
110
111 ## References
112
113 - 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
114 - 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).
115 - [LIANA+ Documentation](https://liana-py.readthedocs.io/)
116 - [LIANA+ GitHub](https://github.com/saezlab/liana-py)