SoptSC for single cell data analysis: unsupervised inference of clustering, cell lineage, pseudotime and cell-cell communication network from scRNA-seq data.
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Updated
Dec 12, 2020 - MATLAB
SoptSC for single cell data analysis: unsupervised inference of clustering, cell lineage, pseudotime and cell-cell communication network from scRNA-seq data.
Infer cell-cell communications based on feed-forward neural network
Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks
scMLnet2.0: Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks
A manually curated database of literature-supported ligand-receptor interactions in human and mouse
characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
Pipeline for simulating CCI dynamics across time
Code used to create the core and extended GBmap, including downstream analyses (cell-cell interactions, spatial transcriptomics deconvolution) and how to produce the figures.
Extracellular vesicle-derived miRNA-mediated cell-cell communication inference for single-cell transcriptomic data
HoloNet. Reveal the holograph of functional communication events in spatial transcriptomics. Help understand how microenvironments shaping cellular phenotypes
Entrain: Predicting Environmental Regulators of Differentiation Trajectories
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
ESICCC: A systematic computational framework for evaluation, selection and integration of cell-cell communication inference methods
Learning cell communication from spatial graphs of cells
Investigate cell-cell signaling, by analyzing ligand-receptor interactions in spatial transcriptomic data
Source code for Liu, Y., Li, J. S. S., Rodiger, J., Comjean, A., Attrill, H., Antonazzo, G., ... & Perrimon, N. (2022). FlyPhoneDB: an integrated web-based resource for cell–cell communication prediction in Drosophila. Genetics, 220(3), iyab235.
LIANA: a LIgand-receptor ANalysis frAmework
Bioinfo scripts for the analyses described in EXPERIMENTAL PROCEDURES section of "Structured wound angiogenesis instructs mesenchymal barrier compartments in the regenerating nerve" manuscript
Spatial direct messaging detected by bivariate Moran
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