LIANA+ provides an all-in-one solution for cell-cell communication inference from single-cell and spatial (multi-)omics data

Processed Datasets

Kuppe et al. (2022): Spatial and single-cell infarction data, obtained via link (Reference: https://www.nature.com/articles/s41586-022-05060-x)
Reichart et al. (2022): Cardiomyopathies, obtained via link (Reference: https://www.science.org/doi/10.1126/science.abo1984)
Carraro et al. (2021): Cystic fibrosis data, obtained via link (Reference: https://www.nature.com/articles/s41591-021-01332-7)
Habermann et al. (2020): Pulmonary Fibrosis data, obtained via link (Reference: https://pubmed.ncbi.nlm.nih.gov/32832598/)
Velmeshev et al. (2019): Single-cell Autism Spectrum Disorder data, obtained via link and link (Reference: https://www.science.org/doi/full/10.1126/science.aav8130)
Wu et al. (2021): Processed breast cancer 10× Visium slides, available at link (Reference: https://www.nature.com/articles/s41588-021-00911-1)
Vicari et al. (2023): Parkinson's disease data, obtained via link (Reference: https://www.nature.com/articles/s41587-023-01937-y)
Russell et al. (2023): Slide-Seq datasets obtained via the Broad Institute Single Cell Portal:

Mouse embryonic brain: SCP2170
Mouse brain: SCP2162
Human brain: SCP2167
Human tonsil: SCP2169, SCP2171
Human melanoma multiome: SCP2176
Also available under GEO GSE244355

(Reference: https://www.nature.com/articles/s41586-023-06837-4)

Kuppe et al. (2022): Acute cardiac infarction, 23 samples, obtained via link (Reference: https://www.nature.com/articles/s41586-022-05060-x)
Reichart et al. (2022): Cardiomyopathies, 126 samples, obtained via link (Reference: https://www.science.org/doi/10.1126/science.abo1984)
Simonson et al. (2023): Ischemic cardiomyopathy, 15 samples, obtained via link (Reference: https://www.sciencedirect.com/science/article/pii/S2211124723000979?via=ihub)
Koenig et al. (2022): Dilated (nonischemic) cardiomyopathy, 38 samples, obtained via link (Reference: https://www.nature.com/articles/s44161-022-00028-6)
Chaffin et al. (2022): Dilated and hypertrophic cardiomyopathy, 42 samples, obtained via link (Reference: https://www.nature.com/articles/s41586-022-04817-8)
Armute et al. (2023): Cardiomyopathies, 40 samples, obtained via link (Reference: https://www.nature.com/articles/s44161-023-00260-8)

Dataset Information

<strong>classification.tar.xz</strong> contains datasets #1-5 used in the classification task for MOFA+/Tensor-cell2cell (Ext Data Figure 5), while single-cell data from Kuppe et al. (#1), was also used for Figure 5.
<strong>wu_et_al.tar</strong> (#6) contains the 10X visium slides used for the malignancy calling task (Ext Data Figure 2A).
<strong>sma.tar</strong> (#7) contains the spatial metabolome-transcriptome data used for Figure 3 as well as Ext Data Figs 3&amp;4.
<strong>heart_visium.tar</strong> contains the 10x visium slides from Kuppe et al. (#1), used in Figure 5 and Ext Data Figure 2B.
<strong>slidetags.tar</strong> contains the Slide-tags data (#8) used for the co-localisation evaluations shown in Figure 4.
<strong>reliability.tar</strong> contains pseudobulks of heart atlases (#9-14) and shown in Extended Data Figure 7.