R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
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Jan 6, 2024 - R
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cell-cell-communication
Here are 50 public repositories matching this topic...
NicheNet: predict active ligand-target links between interacting cells
rna-seq gene-expression network-inference data-integration single-cell-rna-seq single-cell-omics intercellular-communication ligand-receptor ligand-target cell-cell-communication
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Jun 1, 2026 - R
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
single-cell-analysis spatial-transcriptomics cell-cell-interaction cell-cell-communication microenvironment
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Mar 4, 2026 - R
LIANA+: an all-in-one framework for cell-cell communication
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Jul 16, 2026 - Python
LIANA: a LIgand-receptor ANalysis frAmework
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Aug 7, 2024 - R
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
systems-biology scrna-seq single-cell differential-expression single-cell-rna-seq intercellular-communication ligand-receptor ligand-target cell-cell-interaction cell-cell-communication ligand-receptor-interaction intercellular-signaling
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Aug 12, 2025 - HTML
Learning cell communication from spatial graphs of cells
tensorflow glm cvae encoder-decoder-model gnn scanpy cell-cell-interaction cell-cell-communication squidpy
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Jan 15, 2024 - Python
characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
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Apr 30, 2026 - R
User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
machine-learning bioinformatics rna-seq computational-biology rnaseq single-cell single-cell-rna-seq bulk-rna-seq sc-rna-seq cell-cell-interaction cell-cell-communication
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Mar 28, 2026 - Python
Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data
knowledge-graph single-cell spatial-data-analysis spatial-transcriptomics graph-network cell-cell-interaction cell-cell-communication ligand-receptor-interaction spatially-resolved-transcriptomics
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Jan 17, 2025 - R
Code used to create the core and extended GBmap, including downstream analyses (cell-cell interactions, spatial transcriptomics deconvolution) and how to produce the figures.
single-cell-rna-seq glioblastoma spatial-transcriptomics cell-cell-communication large-scale-data-analytics
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Dec 7, 2022 - Jupyter Notebook
Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics
spatial-data-analysis single-cell-omics transcriptomics-data cell-cell-interaction cell-cell-communication
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Jun 9, 2025 - Jupyter Notebook
R package to do the Ligand Receptor Analysis Visualization
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Jun 23, 2026 - Jupyter Notebook
A manually curated database of literature-supported ligand-receptor interactions in human and mouse
rna-seq database toolkit data-analysis single-cell ligand-receptor cell-cell-interaction cell-cell-communication
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Jul 1, 2024 - R
Spatial direct messaging detected by bivariate Moran
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Jul 16, 2025 - Jupyter Notebook
Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks
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Aug 16, 2021 - R
A permutation-free framework for scalable, robust, and reference-based cell-cell communication analysis in single cell transcriptomics studies
single-cell scrna-seq-analysis cell-cell-communication permutation-free fastccc human-ccc-reference-panel
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May 23, 2026 - Python
Fine-grained Spatial Transcriptomics by integrating paired histology image
weak-supervision spatial-transcriptomics contrastive-learning cell-cell-communication histology-images ligand-receptor-interaction
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Mar 30, 2026 - Jupyter Notebook
HoloNet. Reveal the holograph of functional communication events in spatial transcriptomics. Help understand how microenvironments shaping cellular phenotypes
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Aug 30, 2024 - Python
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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Dec 12, 2020 - MATLAB
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