Nichesphere tutorial data

NicheSphere is an sc-verse compatible Python library which allows the user to find differential co-localization domains / niches based on cell type pair co-localization probabilities in different conditions. Cell type pair co-localization probabilities can be obtained in different ways, for example, through deconvolution of spatial transcriptomics / PIC-seq data (getting the probabilities of finding each cell type in each spot / multiplet) ; or counting cell boundaries overlaps for each cell type pair in single cell spatial data (MERFISH , CODEX …). It also offers the possibility to look at biological process based differential communication among differential co-localization domains based on Ligand-Receptor pairs expression data. In our first example on Differential co-localization and process based differential communication analysis, we will use data from the Myocardial Infarction atlas from Kuppe, C. et. Al., 2022 to find differential co-localization domains and underlying differential cell - cell communication networks related to ischemia: Full dataset: FileName: PILOT_tutorial/heart_MI_ST_SC_23samples.h5muModalities: ST+scRNAseqPhenotypes: 'border', 'fibrotic', 'ischemic', 'myogenic', 'remote'Filtering: minimum 1500 cells per sample Annotation (for scRNAseq modality, mudata['sc']): - mudata.obs column: "cell_type": 11 - mudata.obs column: "cell_subtype2" 33 Phenotype (in scRNAseq modality, mudata['sc']): - mudata.obs column: "sampleType" Phenotype based ID (in both modalities, mudata['sc'] and mudata['visium']): mudata.obs column: "patient_region_id" Database: Now loaded from NicheSphere. Nichesphere fibrosis related database contains ligands related to the biological processes below: Process Database Number of ligands Collagens Matrisome (PMID:36399478) 45 ECM affiliated Matrisome (PMID:36399478) 129 ECM glycoproteins Matrisome (PMID:36399478) 168 ECM regulators Matrisome (PMID:36399478) 204 Proteoglycans Matrisome (PMID:36399478) 36 SecretedFactors Matrisome (PMID:36399478) 265 Chemokine Cytosig (PMID:34594031) 42 Cytokine Cytosig (PMID:34594031) 86 GrowthFactor Cytosig (PMID:34594031) 130 Inhibitory Cytosig (PMID:34594031) 36 The rest of data files are explained along the tutorials.