a computational framework to identify and characterize cell niches from spatial omics data at single-cell resolution
☆53Aug 11, 2025Updated 8 months ago
Alternatives and similar repositories for scNiche
Users that are interested in scNiche are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆10Dec 17, 2025Updated 4 months ago
- BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …☆78Nov 13, 2025Updated 5 months ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆171Mar 16, 2026Updated last month
- BayesTME: A reference-free Bayesian method for analyzing spatial transcriptomics data☆14Apr 29, 2025Updated last year
- CellLENS: Cross-domain information fusion for enhanced cell population delineation in single-cell spatial-omics data☆35Jul 24, 2025Updated 9 months ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms☆48Oct 22, 2025Updated 6 months ago
- Deep fusion of spatial transcriptomics and histology images for interpretable high-definition embedding mapping☆18Apr 12, 2026Updated 2 weeks ago
- SPatial INtegration of spatially resolved transcriptomics datasets☆18Mar 14, 2025Updated last year
- ☆34Feb 25, 2025Updated last year
- An R package for fast topic inference to identify tissue architecture in multiplexed images☆16Mar 1, 2026Updated 2 months ago
- Code for the spatial transcriptomic paper on IPF lungs☆22Jul 18, 2024Updated last year
- ☆33May 4, 2025Updated 11 months ago
- ☆17Feb 20, 2025Updated last year
- Python code for cross-condition label refinement in single-cell data with HiDDEN☆14Sep 21, 2024Updated last year
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Identification of spatial homogeneous regions☆21Oct 6, 2025Updated 6 months ago
- The current study provides a comprehensive insights into the PDAC metastatic biology.☆25Aug 3, 2024Updated last year
- Hotspot cluster distance analysis in spatial transcriptomic data☆37Feb 10, 2025Updated last year
- Methods for decontamination of single cell data☆62Feb 16, 2025Updated last year
- Gene group activity utility functions for Scanpy☆101Dec 21, 2024Updated last year
- ☆19Jul 30, 2024Updated last year
- The source code for "High-Parameter Spatial Multi-Omics through Histology-Anchored Integration"☆33Apr 17, 2026Updated 2 weeks ago
- ☆69Sep 16, 2025Updated 7 months ago
- ☆61Feb 13, 2026Updated 2 months ago
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- ☆53Oct 9, 2025Updated 6 months ago
- Learning meaningful representations of genes☆21Jul 7, 2025Updated 9 months ago
- CAST package☆44Oct 26, 2024Updated last year
- Comprehensive analysis of single cell RNAseq and spatial transcriptomics in human acute and chronic wounds☆15Mar 19, 2025Updated last year
- Integration of gut cell atlases☆35Oct 29, 2025Updated 6 months ago
- Network analyses of single cell-based digital twins for personalized treatment of inflammatory disease☆15Mar 23, 2024Updated 2 years ago
- an SRT simulator for simulating multiple spatial variability in spatial resolved transcriptomics and generating unbiased simulated SRT da…☆29Mar 11, 2025Updated last year
- NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.☆24Jun 10, 2025Updated 10 months ago
- Quantifying metabolism activity at the single-cell resolution☆173Feb 18, 2026Updated 2 months ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- ☆13Jan 23, 2025Updated last year
- ☆137Apr 24, 2024Updated 2 years ago
- ☆47Apr 8, 2025Updated last year
- ☆19Nov 24, 2024Updated last year
- ☆37Oct 22, 2025Updated 6 months ago
- ☆132Feb 11, 2024Updated 2 years ago
- Profile purification of single-cell spatial transcriptomics data☆31Nov 13, 2025Updated 5 months ago