ArticleBioinformatics (Oxford, England)2023
Comprehensive visualization of cell-cell interactions in single-cell and spatial transcriptomics with NICHES.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.
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81 citing papers in PubMed.
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- Decoding Multicellular Communication Motifs from Spatial Transcriptomics with ALARMIST.bioRxiv : the preprint server for biology · 2026Article
- CytoSignal detects locations and dynamics of ligand-receptor signaling at cellular resolution from spatial transcriptomic data.Nature genetics · 2026Article
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- Progenitor Resilience and the Early Onset of Chronic Lung Diseases: NHLBI workshop report.American journal of respiratory cell and molecular biology · 2026Article
- Empowering multifaceted analysis of spatial transcriptomics data with RGAST.Briefings in bioinformatics · 2026Article
- Robust identification of cell-cell communication heterogeneity in single cells.bioRxiv : the preprint server for biology · 2026Article
- Artificial Intelligence for Spatial Immunometabolic Analysis of the Tumor Microenvironment: Current Evidence and Future Directions.Current issues in molecular biology · 2026Review
- Spatially decoding genotype-associated epigenetic landscapes in human lymphoma FFPE tissues via epi-Patho-DBiT.Nature communications · 2026Article
- Vascular Endothelial Growth Factor-D Improves Lung Vascular Integrity During Acute Lung Injury.Circulation research · 2026Article
- Pulmonary organoid models demonstrate compositionally driven epithelial plasticity and immune polarization.iScience · 2026Article
- Tracing cell communication programs across conditions at single cell resolution with CCC-RISE.bioRxiv : the preprint server for biology · 2026Article
- scComm: a contrastive learning framework for deciphering cell-cell communications at single-cell resolution.Genome biology · 2026Article
- T cell receptors for antigen on intraepithelial cytolytic T lymphocytes in celiac disease engage enterocyte HLA-E and HLA-B.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
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- Spatial transcriptomics reveals organizational properties of mouse spinal cord and alterations in neuropathic pain.bioRxiv : the preprint server for biology · 2026Article
21 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
motivationRecent years have seen the release of several toolsets that reveal cell-cell interactions from single-cell data. However, all existing approaches leverage mean celltype gene expression values, and do not preserve the single-cell fidelity of the original data. Here, we present NICHES (Niche Interactions and Communication Heterogeneity in Extracellular Signaling), a tool to explore extracellular signaling at the truly single-cell level.
resultsNICHES allows embedding of ligand-receptor signal proxies to visualize heterogeneous signaling archetypes within cell clusters, between cell clusters and across experimental conditions. When applied to spatial transcriptomic data, NICHES can be used to reflect local cellular microenvironment. NICHES can operate with any list of ligand-receptor signaling mechanisms, is compatible with existing single-cell packages, and allows rapid, flexible analysis of cell-cell signaling at single-cell resolution. AVAILABILITY AND IMPLEMENTATION: NICHES is an open-source software implemented in R under academic free license v3.0 and it is available at http://github.com/msraredon/NICHES. Use-case vignettes are available at https://msraredon.github.io/NICHES/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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