Combining single-cell (scRNAseq) and spatial transcriptomics (ST) could give unprecedented molecular disease understanding at single-cell resolution. A more comprehensive analysis of the cell-specific ligand-receptor (L-R) interactions could provide pivotal information about si...
LIANA: a LIgand-receptor ANalysis frAmework. Contribute to saezlab/liana development by creating an account on GitHub.
CSOmap reconstructs cellular spatial organization of individual cells from scRNA-seq data based on three principles: (1) cellular spatial organization is determined by ligand-receptor mediated cellular self-assembly, with cells having high affinity spatially close to each other; (2) the affinity of ...
cella_cellbIf explore the pathway enriched by paired ligand-receptor dataset between sender cellA and receiver cellB, user can set cella_cellb="A-B". 2.3 Visualization CellCall offers a rich suite of visualization tools to intuitively present the results of the analysis, including heatmap, Circo...
1a; “Methods” section), which can well account for the spatial association, i.e., the spatial co-expression of ligand and receptor here. This method is an extension of the well-known Moran’s I in uni-variate auto-correlation analysis24 to a bivariate setting initially by Wartenberg25 ...
(IHC).Bioinformatic analysis was performed based on bulk-seq data from the Cancer Genome Atlas(TCGA)-KIRC and single-cell RNA-seq data from scRNASeqDB and PanglaoDB.Results showed that high CXCL13 expression in TME was associated with shorter progression-free survival(PFS),disease-specific ...
A quantile expression value of the ligand–receptor to represent 𝐿𝑖,𝑘Li,k and 𝑅𝑗,𝑘Rj,k can be chosen to lower the influence of the dropout of the scRNA-seq data [11]. 2.2. Pathway Enrichment Analysis CellCallEXT includes pathway enrichment analysis to identify pathways ...
A Comprehensive Analysis of Fibroblast Growth Factor Receptor 2b Signaling on Epithelial Tip Progenitor Cells During Early Mouse Lung Branching Morphogenesis. Front. Genet. 2019, 9, 746. [Google Scholar] [CrossRef] Jones, M.R.; Lingampally, A.; Wu, J.; Sedighi, J.; Ahmadvand, N.; ...