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-interaction
Here are 23 public repositories matching this topic...
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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Apr 16, 2025 - 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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Jan 14, 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
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
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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Jun 14, 2024 - Python
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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May 13, 2025 - Jupyter Notebook
Spatial analysis toolkit for single cell multiplexed tissue data
tissue network spatial-analysis hotspot single-cell heterogeneity spatial-distribution cell-cell-interaction spaital-analysis imaging-mass-cytometry multiplexed-ion-beam-imaging spatial-omics
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Sep 2, 2024 - Python
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
HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇
image-processing proteomics phenotyping multichannel single-cell spatial-data-analysis ome-tiff cell-segmentation whole-slide-imaging proteomics-data-analysis digital-slide-archive cell-cell-interaction multiplexed-imaging multiplexed-imaging-analysis mibiscope spatial-biology
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Feb 29, 2024 - JavaScript
Extracellular vesicle-derived miRNA-mediated cell-cell communication inference for single-cell transcriptomic data
scrna-seq-data mirna single-cell-rna-seq exosomes extracellular-vesicles cell-cell-interaction cell-cell-communication microvesicles
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Apr 15, 2025 - HTML
Links to interesting courses, tutorials, papers, software etc. related to single-cell omics data analysis
single-cell spatial-transcriptomics trajectory-inference cell-cell-interaction pseudotime-estimation gene-regulatory-network-inference
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May 26, 2024
Infer and visualize cell-cell communication for single-cell RNA-seq data
single-cell-rna-seq single-cell-analysis cell-cell-interaction cell-cell-communication ligand-receptor-interaction
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Jan 11, 2025 - HTML
Multi-level Graph Autoencoder (GAE) to clarify cell cell interactions and gene regulatory network inference from spatially resolved transcriptomics
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Jan 9, 2025 - Jupyter Notebook
Steamboat is an interpretable framework to study multiscale cellular interactions in tissues
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May 4, 2025 - Python
Infer cell-cell communications based on feed-forward neural network
deep-learning single-cell-rna-seq single-cell-analysis feed-forward-neural-networks cell-cell-interaction cell-cell-communication
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Dec 21, 2020 - R
Project on ABM tumor growth for the Agent-Based Modeling course at the UvA 2023-2024
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Oct 10, 2024 - Python
SpaCCI: Spatially Aware Cell-Cell Interaction Analysis
spatial-transcriptomics cell-cell-interaction cell-cell-communication ligand-receptor-interaction visium-st spot-level
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Jan 20, 2025 - R
Spatially-resolved Chimeric AnalyzeR
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Apr 22, 2025 - R
Differential communication analysis for scRNAseq datasets based on expression products
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Aug 14, 2024 - R
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